The MEME Suite
Motif-based sequence analysis tools
MEME Suite Release Notes
MEME version 5.0.4
-
Bug fixes:
- Fixed CentriMo bug: crashed if a motif was as wide or wider than the sequences; now it skips the motif and prints a warning.
- Fixed AMA/GoMO bug: could crash if the motif was very wide.
- Fixed AME bug: could crash if there was only one sequence in the input.
- Fixed SpaMo bug: memory leak would exhaust memory with big input files.
- Fixed FASTA bug: read_one_fasta was failing to leave room for trailing null in read buffer.
- Fixed Tomtom bug: would crash if primary motif was not valid.
- Fixed MCAST bug: would crash if any sequences was shorter than the widest motif.
- Fixed MCAST bug: would crash if any motif was only 1 wide; now motifs are skipped if
their width is less than 2.
- Fixed MCAST bug: would sometimes crash when --synth switch given. MCAST
results are now slightly different (different p-, E- and q-values, mostly.)
- Fixed MCAST bug: crash could occur when there was only one or two motifs.
- Fixed MCAST bug: output would not display properly sometimes when the number of motifs
was very large.
- Fixed CentriMo bug: would crash if any motif was as long as the sequences; now motifs
are skipped if they are not at least 2 shorter than the sequences.
- Fixed missing documentation files fasta-center.html and fasta-dinucleotide-shuffle.html.
-
Improvements
- AME: Checks that there are a total of at least 2 primary and control sequences.
- AME webserver: Checks that there are a total of at least 2 primary and control sequences.
- CentriMo webserver: Added option to use a uniform background model, or the model in the motif file.
- MCAST webserver: Added option to not hard-mask (convert to 'N') lower-case nucleotides.
- MEME webserver: Checks that there are at least 2 primary sequences unless you specify
the 'Any Number of Repetitions' site distribution.
- SpaMo webserver: Added advanced option to specify the background model.
- MEME: reduce the amount of memory required, especially with the ANR model. With ANR,
no more than 2,000,000 local maxima will ever be stored (1,000,000 each for primary and
control sequences).
- FASTA input: programs will now skip sequences that are too long, rather than dying.
- test_driver: added --valgrind switch to allow search for memory leaks.
- Plugged many memory leaks.
-
Documentation
- MEME: Clarify that -nsites and -maxsites override -csites if the model is ANR,
and correct the description of the default for -maxsites.
MEME version 5.0.3
-
Bug fixes:
- Fixed MAST bug: didn't read E-values of motifs correctly if they were >1e300; checks the log(E-value) of motifs now.
- Fixed MEME bug: -cons option didn't work when the model type is DE or SE.
- Fixed MEME bug: -mod zoops sensitivity was decreased for large datasets (greater than -searchsize)
due to incorrect setting of the initial fraction of sequences with sites.
- Fixed gendb bug: -alph option caused crashing.
- Fixed AME bug: output erroneously called E-value threshold "Adjusted p-value threshold".
- Fixed AME bug: crashed sometimes when sequence names were > 100 characters (bug in shuffle_seq()).
- Fixed bug: parsing of MEME model file alphabet line was failing if they were missing the trailing ":".
- Fixed FIMO bug: crash occurred if a motif in a MEME text file had zero alphabet length.
- Fixed MCAST bug: crash occurred if a motif ID was longer than 50 characters.
- Fixed MEME bug: crash when sequence name contained a non-ASCII character; now replaces them with
underscores.
- Fixed SPAMO bug: crash caused by bug in similar sequence removal algorithm
-
Improvements
- MEME: Improve results with large alphabets by making the default value of "fuzz"
(see MEME option -spfuzz) depend on the alphabet size: fuzz = 2 / size_of_alphabet.
- MCAST: Improved user message when the --hardmask switch is given and lower case letters
are changed to wildcards.
- CentriMo: Improved failure message when the input file contains no sequences of the
correct length.
- MEME-ChiP: Improved documentation to emphasize that motif discovery is only in the
central regions (100 characters by default) of the input sequences;
also removed reference to 50Mb website limit.
- test_driver: Added --valgrind switch to allow testing for memory errors.
MEME version 5.0.2
-
Bug fixes
- Fixed rna2meme bug when there is no word after the FASTA ID.
- Fixed bug that caused failure of notification email for AME web app
- Fixed bug that caused generation of spurious warning message file for AME web app
- Fixed bug that caused miscounting of background peptides in MoMo with MoDL algorithm.
- Fixed bug that caused MEME not to honor the limits on nsites.
- Fixed menu link to MEME SUITE source code.
- Fixed missing Messages file link in MEME-ChIP output.
- Fixed missing output format documentation files.
-
Improvements
- Added -searchsize 0 feature to MEME to make it emulate earlier versions of MEME
when used with -objfun classic.
- Added shuffled foreground peptides as default for MoMo background peptides.
- Greatly improved computation of MoMo E-values.
- Improved MoMo HTML output.
- Added new MoMo TSV output file.
- Added new MoMo test.
- Fixed the momo.html file to give correct descriptions of --min-occurrences,
--remove-unknowns and --eliminate-repeats regarding affect on background peptides.
- Created documentation file 'momo-output-format.html'.
- Fixed the rna2meme documentation file 'rna2meme.html' to corectly describe its purpose.
- Fixed the motif_conversion.html file to give better example of rna2meme.
- Installation now allows the user to specify the URL for a local website, the
alternate local website, and the source code repository.
These locations are then updated throughout the installed command-line and website applications.
If desired, these can all be set to local URLs so that no links will point
outside of the user's installation of the MEME Suite.
- Updated tool output HTML to specify the location of help on interpreting
results and the repository fo downloading the source code as separate URLs.
- Re-formatted FIMO HTML output to resemble the other tools' output.
MEME version 5.0.1
-
Bug fixes
- Fixed bug in momo_webservice with
--remove_unknowns
switch
- Fixed AME bug triggered by sequences that are too short for the
widest motif
- Fixed NULL pointer bug in MEME triggered by
-maxsize
option
- Fixed bug in momo.test
-
Improvements
- Enhancements to MoMo HTML output.
MEME version 5.0.0
- Highlights
- MEME improvements:
- Major speed enhancements have been made to MEME when used with large inputs.
- Two new objective functions have been added to MEME for finding differentially enriched
and centrally enriched motifs, respectively.
- The MEME webserver now allows much larger inputs. Inputs may now contain up to 500,000 sequences
(up from 1000). The input form limit of 80,000,000 characters remains.
- AME improvements: The AME tool has been completely redesigned, its speed enhanced, and many bugs have
been corrected.
- MEME-ChIP improvements:
- MEME-ChIP now uses all input sequences. It no longer subsamples the input sequences if there are more than
600, which was previously needed due to MEME's time complexity with large inputs. The MEME-ChIP webserver
now accepts inputs with up to 500,000 sequences. The input form limit of 80,000,000 characters remains.
- The MEME-ChIP output has been improved, and now provides both an output summary in TSV format as well as
a file containing all the enriched motifs found in MEME format.
- New (TSV) output files: Most tools now also produce tab-separated value format (TSV) output files.
Links to each of the new output files have been added to the top of the tool's HTML output file.
These TSV files simplify and enhance using the output of the tools
AME, CentriMo, FIMO, GOMo, MCAST, MEME-ChIP, SpaMo and Tomtom. Each TSV output file contains
a header line (without the "#" character so R will see the column names as variables).
The main TSV output files also contain the version number, documentation link and command line.
- More documentation: Added documentation files for the output formats of
AME, CentriMo, FIMO, GOMo, MCAST, MEME-ChIP, SpaMo and Tomtom.
The MEME documenation now includes plots of running time as a function of input size.
- Improved documentation:
- Ambiguous characters: Added documentation to each HTML man page stating how the tool treats ambiguous characters in sequences.
- Alphabet description: Added the alphabet description to the HTML output for: AME, CentriMo, SpaMo, MEME-ChIP, MCAST, FIMO, Tomtom.
- Backward compatibility testing: Added backward compatability testing of motif reading in motif-in.test (--comprehensive) for versions
as old as 4.7.0.
- Standard directory structure: The directory structure of the MEME Suite installation now conforms to the
Filesytem Hierarchy Standard.
- Balanced background models: When scanning both strands, all tools now "balance" the background model
(if the alphabet has complements) before using it to create pseudocounts for the motifs.
- Command-line consistency: All programs now also accept -bfile if they just accepted -bgfile before.
- New Features and Enhancements
- AME
- Increased speed by 38%.
- Added a TSV file summarizing the enriched motifs.
- Added a TSV file listing positive sequences for significant motifs (Fisher only).
- Added links to the TSV files at top of HTML output.
- Made p-value computations in log space.
- Replaced the option --pvalue-threshold with option --hit-odds-fraction,
which defines hits as having scores at least X% of the maximum
possible score for the motif. Whereas --pvalue-threshold only
applied to the totalhits scoring method, --hit-odds-fraction applies
to all scoring methods.
- Removed option --pwm-threshold. The positive sequence score threshold
for the fisher method now uses the --hit-odds-fraction option.
- fisher method: now performs optimization over sequence score thresholds
in --fix-partition or --control modes.
- linreg method: renamed to 'pearson', it now computes p-values and optimizes the p-value of the
Pearson's correlation coefficient, rather than mean squared error.
- spearmans method: now does partition maximization and computes p-values.
- Report p-value adjusted for number of tests and E-value (adjusted for number of motifs)
instead of raw p-value and p-value adjusted for tests+motifs.
- Changed --pvalue-report-threshold to --evalue-report-threshold.
- Removed --linreg-normalize and --rs-method options.
- Added Pos, Neg, %TP, %FP and Score columns to Fisher test output.
- Changed "--method mhg" to "--method 3dmhg".
- Removed "--bgformat" option and made selection of background model identical to CentriMo's method.
- Changed the default pseudocount to 0.1 (like CentriMo) and changed the option.
from "--pseudocount" to "--motif-pseudo" (like CentriMo).
- Added --shuffle-- keyword to --control option, causing shuffled primary sequences
to be used as the control sequences.
- Added --kmer switch to cause -mers frequencies to be conserved when shuffling.
- Added --seed to allow the random number seed to be set.
- Added --inc and --exc switches to allow choosing motifs whose names match a pattern.
- Created documentation file 'ame-output-format.html'.
- AME Website
- Added "NONE" as choice for control sequences.
- Added all remaining association functions to menu: linear, spearman, 3dmhg, 4dmhg.
- Changed default association function to "fisher".
- CentriMo
- Changed centrimo.txt to centrimo.txv, a TSV file summarizing the enriched motifs.
- Added links to the TSV files at top of HTML output.
- Created documentation file 'centrimo-output-format.html'.
- Added "Concentration" field to HTML output, which gives the total probability
in the central region whose size is controlled by the user-adjustable "smoothing window" size.
- added --inc and --exc switches to allow choosing motifs whose names match a pattern.
- added --dist switch to perform distance-to-center-of-sequence motif enrichment analysis.
- added --use_pvalues switch to allow thresholding on the adjusted motif p-value rather than the log-odds score.
- removed --dist switch because it was not useful.
- DREME
- Changed the -v option to -verbosity to match other tools in the MEME Suite.
- Added documentation on the sequence logo files created by DREME.
- FIMO
- Changed fimo.txt to fimo.tsv.
- Added links to TSV and GFF3 output in HTML output.
- FIMO Website
- Removed non-functional user interface elements for submitting a custom alphabet file from web application.
- GOMo
- Changed gomo.txt to gomo.tsv, a TSV file summarizing the enriched motif-GO term pairs.
- Added header line to the TSV output.
- Added links to TSV and XML output in HTML output.
- MAST Website
- Removed non-functional user interface elements for submitting a custom alphabet file from web application.
- MEME
- Improved MEME's speed.
- MEME's running time is now now O(N) for the OOPS model,
and O(N log N) for the ZOOPS model,
where N is the total size of the input sequences.
- Added -maxsize option, which sets the maximum number of characters
from the input sequences that will be used during EM, the second
step of MEME. (All data is used in the final, discretization step.)
This reduces the time complexity of the second step of MEME
to a constant not dependent on the size of the input sequences.
- Added -csites option, which sets the maximum number of sites allowed
for motifs when using the "Classic" MEME objective function.
By default, the limit is 1000 sites. Increasing this can
increase running time substantially due to the cost of computing
the value of the "Classic" objective function
for motifs with many sites (time = O(#sites^3)).
- Added documentation on the sequence logo files created by MEME.
- Enhanced MEME with new objective function for finding differentially enriched motifs.
- This objective function causes MEME to search for motifs that are enriched
in the primary sequences relative to the control sequences.
- New objective function is selected using the -objfun option: -objfun de
- The user may provide a set of control sequences via the -neg option;
otherwise MEME will create a control set of sequences by
shuffling the primary sequences.
- Added -shuf option, which controls the size of words whose frequencies
are preserved when shuffling sequences to create a control set.
- Motif significance is computed using the multiple hypergeometric test,
which is substantially faster than the "Classic" MEME objective function,
and yields less conservative E-values.
- Enhanced MEME with new objective function for finding centrally enriched motifs.
- This objective function causes MEME to search for motifs that are enriched
in the central regions of the sequences, which must all be of thes ame length.
- New objective is selected using the -objfun option: -objfun ce
- Motif significance is computed using the binomial test,
which is substantially faster than the "Classic" MEME objective function,
and yields less conservative E-values.
- This objective function is designed for use with sequences from whole
genome approaches such as ChIP-seq and CLIP-seq, and the sequences should
include adequate flanking region around the expected motif sites--e.g.,
use sequences of 500bp for ChIP-seq.
- Improved MEME's use of background models.
- Added the -markov_order option, which specifies the order of the
background model to generate from the input sequences (default),
or the maximum order model to extract from the file given
using the -bfile option.
- Improved MEME's search for starting points (Classic objective function).
- Added the -use_llr switch, which causes the log-likelihood ratio (rather
than the Classic objective function) to be used in evaluating possible
starting points for EM. This allows for higher order background
models to affect the search for starting points.
- Improved MEME's search for motifs (non-Classic objective function).
- MEME now detects if EM "wanders" away from the starting point
and uses the (discretized) starting point as the motif in that case.
- Other MEME enhancements
- Removed limitation on the number of motifs MEME can report.
- Changed: MEME run from -cons will only try the given width with that start.
- Fixed: computation of background frequencies in MEME when there are ambiguous characters.
- Fixed: changed the default maximum value of -maxnsites to 600 when using the ANR model, matching the
documentation.
MEME Website
- Increased allowed input size: Max sequences now 1,000,000 (from 1000).
- Increased allowed input size: Max letters now 10,000,000 (from 60,000).
- Added ability to create up to 4th order models from the input sequences.
- Added "Differential Enrichment mode" as alternative to "Discriminative mode" (which
uses a position specific prior).
MEME-ChIP
- Removed subsampling from MEME-ChIP--it now uses all the input sequences.
- Created documentation file 'meme-chip-output-format.html'.
- Added '-keepprimary' to command line.
- Added new test for custom alphabet mode.
MEME-ChIP Website
- Added "Differential Enrichment mode" as alternative to "Discriminative mode" (which
uses a position specific prior).
- Added ability to create up to 4th order models from the input sequences.
MoMo
- Added documentation on the sequence logo files created by MoMo.
- Make "no hashing" the default for finding the location of peptides
when a protein database is provided.
SpaMo
- Added feature to output all of the "contributing sequence IDs" as a text or BED file with one click of a button at the top of the output form. Sequence IDs are introduced by a line containing the file name that would be used if the sequence IDs for a single primary-secondary spacing were output.
- Fixed bug in -xalph that caused the wrong background for secondary motifs.
- Fixed bug in HTML display of number of significant motifs when >1 secondary DBs.
- Fixed bug causing number of erased matches to be wrong with -keepprimary.
- Clarified use of -inc and -exc; they only affect secondary motifs.
- Changed TXT file to TSV file summarizing the enriched motifs.
- Added links to the TSV files at top of HTML output.
- Created documentation file 'spamo-output-format.html'.
Tomtom
- Changed text output file name to "tomtom.tsv".
- Added links to TSV and XML output in HTML output.
- Added HTML to smoke tests.
MEME version 4.12.0 -- June 27, 2017
-
Enhancements
-
Added MoMo application.
MoMo identifies sequence motifs associated with different types of protein post-translational modifications (PTMs).
The program takes as input a collection of PTMs identified using protein mass spectrometry.
For each distinct type of PTM, the momo command uses one of three algorithms to constructs a motifs
representing amino acid preferences flanking the modification site.
-
Bug fixes
-
Fixed default values for centrimo options
--score
and
--motif-pseudo
.
MEME version 4.11.4 patch 1 -- May 18, 2017
-
Bug fixes
-
Fixed bug in Tomtom that disabled the -png and -eps options.
-
Fixed bug in fasta-hamming-enrich with non-complementable alphabets.
-
Enhancements
-
Improved documentation on background file inputs
for AME, MEME, MEME-ChIP, MAST, Centrimo, and Tomtom.
- Added the reverse complement as the alternate ID in iupac2meme.
- Added documentation for meme2images script.
MEME version 4.11.4 -- March 31 2017
-
Enhancements
- AMA GFF2 output now has only 9 fields as in the standard, and
the AMA documentation has been corrected to reflect this.
- MEME motif names are now their consensus sequence,
rather than a number, and the alternate ID is "MEME-i", where
"i" = 1, 2, 3,... is the old motif name. MEME tests now check the integrity of
all output formats: text, HTML and XML.
- DREME motifs now include an alternate ID "DREME-i", where
"i" = 1, 2, 3... etc. is the index of the motif.
- CentriMo output now contains a column for the motif consensus sequence,
and the display of this column can be turned on or off.
- MEME-ChIP now produces a summary file
in "tab-separated values" format suitable for use by programs such as Excel
and for easy parsing by scripts.
The motif IDs in this file are synchronized with the IDs in the motif file
named "combined.meme" file, which contains all of the significant motifs
found by MEME-ChIP in MEME Motif Format.
New links to these two files are provided at the top of the
of MEME-ChIP's HTML output.
The HTML output of command-line MEME-ChIP is now named "meme-chip.html", as it was
for the web-server version. The --index-name option has been removed.
- FIMO output now includes a column for the alternate motif name. Added command line
to XML output. Different FIMO tests check input of all three MEME formats: text, HTML and XML.
Added the sequence name and strand to the "Group Name" field in GFF3 output so
that GFF3 files can work with the UCSC Genome Browser, which requires groups members
to all be on the same sequence and strand.
- Motiph Added command line to XML output.
- MAST text output (including with the -hit_list option) now includes columns
for the motif name and alternate name in addition to the motif index.
- AME --bfile option now overrides --bformat so it is only necessary
to specify --bfile to get the desired result.
- AME output now includes a column for the alternate motif name;
in addition, the text output also includes the consensus of the motif.
- SpaMo Fixed alignment of inferred secondary logo when the secondary logo
was trimmed on the left. Added the alternate ID wherever the motif ID is displayed.
Replaced spaces with underscores in the Inferred Secondary and Alignment motif names
when they are downloaded as MEME motifs or EPS images. Documented the problem
with Macs not showing the scroll bar under the Alignment logos.
- GOMo Fixed bug causing webserver page to crash if no GOMo databases are installed.
MEME version 4.11.3 patch 1 -- March 11, 2017
-
Bug fixes
-
Fixed bug causing FIMO not to generate GFF output for motifs using
RNA or custom alphabets.
-
Fixed bug that caused MEME-ChIP to halt with an error when TomTom finds no matches.
-
Fixed bug that caused MEME Suite build and install to fail when no system copy
of the XSLT library was installed.
- Fixed Java 8 incompatibility in web site installation.
MEME version 4.11.3 -- February 21, 2017
-
Enhancements
- Added AME, DREME, and FIMO tutorials.
- Improved consistency and documentation of -alph, -xalph and --bfile/-bgfile options across the MEME Suite.
-
Bug fixes
-
Fixed bug causing MEME-ChIP to fail to show "Known or Similar Motifs" for MEME and DREME
MEME version 4.11.2 patch 2 -- October 24, 2016
-
Enhancements
- Added support for Python 3.
-
Bug fixes
-
Fixed bug causing MEME-ChIP to fail to show "Known or Similar Motifs" for MEME and DREME
de novo motifs.
-
Fixed bug in handling of RNA-like custom alphabets.
-
Fixed bug in MAST -comp option.
MEME version 4.11.2 patch 1 -- June 16, 2016
-
Bug fixes
-
Fixed bug in MCAST 4.11.2 that caused it to prematurely truncate
reading the sequence file.
-
Modified MEME to fall back to a simple Dirichlet prior when
using DNA or a custom alphabet with a prior that requires
a prior library, but no prior library is specified.
MEME version 4.11.2 -- May 5 2016
- Enhancements
-
Reduced running time of DREME by 60%.
-
Improved running time of FIMO.
-
Added Ensembl Fungi, Ensembl Metazoa, Emsembl Protists, and
Ensembl Plants to on-line sequence databases.
-
Improved links to on-line annotations in MAST results.
-
Added
fasta-re-match
script for scanning FASTA files
with regular expressions.
-
Updated installation guide.
MEME version 4.11.1 -- Jan 15 2016
- Bug fixes
-
Script tag 'src' attributes for web applications now include
a 'version' parameter to prevent outdated scripts from being cached.
-
The C standard
gnu89
is specified for the build.
This resolves problems building the MEME Suite with GCC 5.1.
This was a common problem for users running the
latest version of Ubuntu.
-
Fixed incorrect formatting of E-value threshold in MEME XML output.
The incorrect formatting caused failures in
meme_xml_to_html
.
-
Fixed error in TomTom web application when the RNA alphabet was
selected.
-
Fixed error in Javascript alphabet parser.
The parser was not allowing blank lines,
or lines consisting only of a comment.
-
Fixed error in fasta-center and psp-gen scripts that prevented use of RNA
alphabet.
-
Fixed errors in specification of options, and parsing errors in
elm2meme script.
-
Removed broken link to LAM MPI.
LAM MPI has been superseded by Open MPI,
and the host web site no longer exists.
MEME version 4.11.0 -- Nov 23 2015
- New Features and Enhancements
- Custom alphabet support
- A majority of the programs in the MEME Suite now support
custom alphabets including MEME, DREME, MEME-ChIP, CentriMo,
SpaMo, AME, FIMO, MAST and Tomtom.
- RNA has been added to the list of built-in alphabets.
- Priors for sequence databases
- The FIMO and MCAST web services now have support for position
specific priors for some selected databases.
- SpaMo
- Sensitivity is improved by combining the counts for secondary motif sites in each
of the four possible orientations in 9 ways corresponding to patterns
expected when the primary and/or secondary motif is palindromic.
- Sensitivity is improved by using all secondary motif sites scoring above the score threshold
in the analysis rather than just the best-scoring site. The old SpaMo approach
can still be used by specifying the new "-usebestsec" switch.
- False positives are reduced because, by default, all occurrences
of the primary motif are "erased" (other than the central one).
This reduces the tendency of motifs similar to the primary
motif to appear enriched. The -keepprimary switch can be used
to override this behavior so that spacings between multiple
occurrences of the primary motif can be observed.
- The sequence identifiers for the sequences with the significant spacing
are now displayed to allow further downstream analysis (e.g., GO or pathway analysis).
- The actual secondary sites are combined into an "inferred motif" and displayed
as a sequence logo in order to
make clearer what the putative sites look like. This allows cases where
the significant secondary motif in the database is similar, but not the same,
as the motif actually present in the sequences.
- The inferred motif is displayed as a frequency matrix to allow further
downstream analysis (e.g., using Tomtom to search other motif databases
to identify motifs more similar to the inferred motif.
- Alignments of the sequences with the significant spacing are displayed as
sequence logos. Among other purposes, this can allow cases where the
sequence similarity extends beyond or between the primary and secondary sites,
suggesting either 1) the regions are repetitive or 2) the actual secondary
or primary motif sites are distinct from the respective primary and secondary
motifs used in the analysis.
- The elimination of overly similar sequences has been sped up using a
heuristic optimization. A bug was also eliminated that caused the
comparison to involve only the given strands of DNA sequences rather
than both strands.
- By default, all sequences containing ambiguous characters in the margins
around the primary motif are now removed. This is necessary for the
new heuristic similarity search. It also helps insure that the
uniformity assumption of random motif occurrences since sites with
ambiguous characters are not scored. This check is turned off when
the similarity search is disabled using the "-shared" switch.
- A tab-delimited text output file "spamo.txt" is now created for
easy parsing by other programs.
- The new -text switch causes SpaMo to create only the text
file "spamo.txt", skipping the creation of the HTML output file.
- Changed handling of duplicate sequence IDs from 'die' to 'skip'.
- fasta-shuffle-letters
- Added capacity to perform efficient, higher-order
shuffling of FASTA sequences.
- Bug fixes
- taipale2meme
- Changed naming of multiple motifs for
same TF to start with _1 (rather than no _).
- Fixed bug that was giving motifs duplicate
names when _2 was reached.
MEME version 4.10.2 -- Aug 11, 2015
- New Features and Enhancements
- General
-
Added the utility script
fasta-grep
for finding matches to a Perl regular expression
in a FASTA file.
- Replaced use of system pseudo-random number generator
with an implementation of Mersenne Twister, providing
more consistent results across platforms
- File conversion utilities
- Added
-seed_start
, -seed_end
and -other_count
options to rna2meme
- FIMO
- Eliminated dependency on XSLT for output
- MCAST
- Added support for Position Specific Priors (PSP)
- Improved modeling of p-value distribution: GC content added as a
parameter in EM estimation of exponential distribution.
- Eliminated dependency on XSLT for output.
- Web pages
- Added a job submission rate limiter to the web server
- Added additional check to all job submission forms to ensure
the combined form input size is smaller than 80MB
- Added links for viewing the load on the alternative servers
- Improvements to the display of sequence and motif databases
- sequence-update database utility
- Numerous enhancements and fixes
- Bug fixes
- Documentation
- Numerous documentation fixes and improvements
- General
- Added check for sequences shorter than the motif
used to scan them
-
Fixed the parsing of MEME motif files to handle cases when the
E-values are written out in different formats
- Fixed the writing of MEME motif files so the
E-values are written out using the same formatting in (hopefully) all circumstances
- Web pages
- Fixed the logic used to display server news and notices
to take into account differences between the clock of the server
and the local computer's clock.
- Fixed a bug where the webserver was not logging
the job submission times
- Fixed a bug in the website FASTA file validator
which was incorrectly rejecting sequence weights for being out of range
- Added more obvious links to the motif database
overview page from the job submission pages
- Changed download page to prevent caching of the inner frame
in the Safari web browser
- Fixed handling of non-ASCII input on all web-forms
- Fixed a server error caused by the absence of cookies.
- Made disallowed alphabets for sequence inputs on web forms
more obvious by using a red cross-out over the names
- Fixed inclusion of example files for GLAM2 and minimal
MEME motifs for the website install
-
Improved the error message the MEME reports
when given a single sequence without using "any number of repeats" (ANR) mode
- Fixed incorrect URL in RSAT downloader configuration
- AME
- Fixed bug causing segfault
-
Fixed bug causing the maximum motif width to be incorrect
resulting in a dependency on motif order
- Fixed failure to generate log files
- GLAM2
-
Fixed generation of sequence logos for GLAM2 motifs with pure deletion columns
- MAST
- MAST now ignores WEIGHTS section in FASTA files
- Tomtom
-
Fixed submission to Tomtom from GLAM2 DNA output
MEME version 4.10.1 -- Mar 19, 2015
- New Features and Enhancements
- Improved Web Pages
- Updated the schematic on the home page and added more "hover" blurbs
explaining what tools and databases do.
- Created separate man pages for the Web and Command Line versions
of all commands.
- Use same blurb for blurb, web man page and command line man page for each tool.
- Added links to Manual on each tool input form (top right).
- Email address are not required for job submissions.
- Improved test scripts
- Updated the testing scripts to work with Automake's
custom test driver specification.
- Split the tests into a file per program to make maintenance
easier.
- CentriMo
- Added "Region Position" sort to allowing sorting from left to right.
- Renamed "Region Center" sort to "Region Distance".
- FIMO
- Improved the XML to HTML stylesheet.
- MCAST
- Improved the XML to HTML stylesheet.
- SpaMo
- The elimination of overly similar sequences has been sped up using a
heuristic optimization.
- By default, all sequences containing ambiguous characters in the margins
around the primary motif are now removed. This is necessary for the
new heuristic similarity search. It also helps insure that the
uniformity assumption of random motif occurrences since sites with
ambiguous characters are not scored. This check is turned off when
the similarity search is disabled using the "-shared" switch.
- getsize
- Added capacity to perform efficient, higher-order
shuffling of FASTA sequences.
- update-sequence-db
- Added extra configuration file options for updater URLs so
in theory local mirrors can be used.
- transfac2meme
- beeml2meme
- Added ability to use the "NA" line as
the ID and make the consensus letter in
matrix lines optional in order to support
TRANSFAC-like formats (i.e., Swiss Regulon).
- Added ability to process multiple files.
- Added ability to draw alternate ID and URL from a snapshot
of a specific Uniprobe webpage.
- iupac2meme
- Added ability to invert the meaning of a symbol group with '^'.
For example with a DNA motif [A] would match A but [^A] would
match C, G, or T.
- taipale2meme
- Changed naming of multiple motifs for
same TF to start with _1 (rather than no _).
- Fixed bug that was giving motifs duplicate
names when _2 was reached.
- README
- Reformatted the README as Markdown styled text.
- Bug fixes
- Webpages
- Fixed various issues with viewing the website and outputs
in Internet Explorer.
- Sequence uploads
- RNA sequences are now converted to DNA again as was the
behavior in release 4.9.1. This is a temporary fix to avoid
problems in MEME and AME where 'U's were not supported. Support
for custom alphabets is intended for a future release.
- CentriMo
- Ensure rounding up on window sites for the text output.
The text output was using bankers rounding which occasionally
caused different results to the rounding displayed in the HTML
output.
- FIMO
- Fixed PSP reader to honor --parse-genomic-coord option.
- Removed unused --max-seq-length option.
- Changed FIMO to not attempt to rewind the file when reading
from standard input. FIMO will now report an error when you
attempt to scan more than one motif when reading the sequences
from standard input because handing multiple motifs requires
rewinding the file with FIMO's current architecture.
- MEME
- Fixed bug when PSP files contain zeros; 1e-16 is now added to those entries.
- MCAST
- Fixed bugs in purging of low score matches when max stored matched reached.
- Fixed GC ranging and match purging code.
- SpaMo
- A bug was eliminated that caused the sequence similarity
comparison to involve only the given strands of DNA sequences
rather than both strands.
MEME version 4.10.0 -- May 6, 2014
- New Features and Enhancements
- Website
- The side-bar menu was completely rewritten to work in all the
documentation even when the MEME Suite has not been installed.
- Many confusing, extraneous and hard to update summary pages
that the old side-bar menu required have been removed.
- All the command-line documentation has been standardized to
a common pattern which will hopefully make it easier to understand.
- The job submission logic has been rewritten using Java
Servlets instead of Perl CGI scripts. This should enable better
integration with Opal as the Perl interface to Opal had not been
updated with the more recent Opal versions.
- The job submission pages use new techniques to validate
files before you click the submit button.
- All the pages that accept MEME formatted motifs can accept
hand typed motifs using IUPAC codes, lists of sites or
frequency/count matrices.
- MEME
- Removed the shell script that used to be needed to execute serial ('meme.bin') or
parallel ('meme_p') versions of MEME. MEME is now a single executable ('meme') like
the other C-based MEME Suite programs.
- New HTML output with a more compact overview, delayed
loading to handle display of larger sequence counts and a
combined motif site/scan diagram.
- CentriMo
- New feature in output to plot site probability vs. distance from center of sequence.
- MEME-ChIP
- Print value of
-filter-thresh
in header of MOTIFS section of output.
- AME
- Added web interface to the AME "Analysis of Motif Enrichment" tool.
AME reports (known) motifs that are enriched in your input nucleotide sequences
compared with either (a) shuffled versions of your sequences or (b)
control sequences that you supply.
- Correct Fisher's Exact test to be one-tailed rather than two-tailed so
that under-represented motifs don't get small p-values.
- Disable "better" ranksum test mode (it's broken).
- rna2meme
- Allow reading from standard input if input filename is '-'.
- Sequence Databases
- Added more sophisticated tool for server operators to
download sequence databases.
- Added UCSC Mammal Genome sequence databases.
- Sequence databases are now versioned where possible and timestamped where not.
You can select the desired version for search via MAST, FIMO, MCAST or GLAM2SCAN.
MEME version 4.9.1 -- August 23, 2013
- New Features and Enhancements
- AME
- Make "overwrite directory ame_out" default behavior like other MEME Suite programs.
- Change test on --pvalue-report-threshold from "<" to "≤".
- Add help popups for Split, p-value and Corrected p-value.
- CentriMo
- Added the ability to scan with the reverse complement
of each motif separately (--sep). This is useful when
the sequences have strand information (e.g., TSSs) and the
motif has a preferred orientation.
- Added the ability to limit the minimum size of regions
whose significance is computed (--minreg). This allows
the user to restrict regions to a width range so that the
significance levels of all motifs can be compared for
regions of the same size.
- Added the ability to zoom-in on a section of the output graph.
- DREME
- Add "Time" to end of text output file.
- MCAST
- Move "display more" arrow in HTML output to left (same as MAST output).
- MEME-ChIP
- Documented the -group-thresh and -group-weak switches; changed
default -group-weak threshold to be only 2 times (not 10 times)
the -group-thresh to avoid excessive merging of motif clusters.
- The number of motifs to be found by MEME or DREME may
now be set to zero on the command line
to prevent either of the programs from being
run. CentriMo and the motif clustering algorithm will still
be run, allowing MEME-ChIP to be used as a front-end to CentriMo.
- Add -centrimo-flip option so that matches on reverse strand
will be reflected around center of sequence. This permits
(non-palindromic) motifs with asymmetric binding to be detected.
- Added -meme-maxsize option to expose MEME's maxsize option.
- SpaMo
- The (slow) sequence redundancy step can now be skipped
by setting the --shared option to zero.
- Added extra documentation recommending the use of a
repeat-masker before running SpaMo.
- Other
- The utility fasta-get-markov is now implemented in c
and is much faster than before. It is backwards compatible
with the Perl implementation but now has some new features
like the ability to specify input and output files,
a progress display and summary of the sequence
counts/sizes like from getsize.
- Implemented a better hashing function for use by the
hash table datastructure which should improve performance
and also fix an overflow bug that was present in the
old function.
- Script fasta-fetch now handles sources with genomic coordinates that list negative strands.
- Disabled building of obsolete programs and made an effort to remove unused "fossil" code.
- Enforced separation of library and program code so Python and Perl libraries
should no longer be installed into the bin directory.
- Added a link to the MEME Suite's Google Scholar page from the citing page.
- Improved resiliency of get_db_csv to poorly behaved FTP servers.
- Bug fixes
- AME
- Fixed usage message to include defaults.
- Fix bug in computation of corrected p-value (LOGEV).
- Fixed a bug where short sequences combined being scanned
with long motifs could cause the program to attempting
scanning before the sequence start and into unallocated
memory.
- CentriMo
- Fixed bug causing log-odds scores of "N" columns to be non-zero in CentriMo.
- Increased accuracy of log-odds scores in CentriMo by upping PSSM_RANGE.
- Fixed off by 0.5 error in output graph where the graph was shifted right by half a unit.
This error wasn't noticeable until we added the zooming feature.
- Now only creates links to motifs that have URLs.
- DREME
- Fixed a bug where DREME would crash when it couldn't find Ghostscript.
- FIMO
- Fixed bug where FASTA sequence IDs were truncated at ":" if they looked like BED format.
- Fixed bug with all "N" motifs causing crash.
- Fixed bug causing log-odds scores of "N" columns to be non-zero in FIMO.
- Fixed bug causing free of unallocated memory.
- Fixed bug where the release date would be truncated in output.
- Increased accuracy of log-odds scores in FIMO by upping PSSM_RANGE.
- MAST
- Fixed the output's display of the background model when the sequence composition was used.
- Corrected a link to an example motif file on the job submission form.
- MCAST
- Fix MCAST bug: wasn't printing motif match threshold.
- MEME
- Fixed memory link and double free when
-cons
option was used.
- MEME-ChIP
- Fixed a bug where a motif could be discovered by MEME but excluded by MEME-ChIP due to a large E-value
and then be rediscovered by CentriMo by being centrally enriched. This sequence of events would cause the
output to break as the Javascript made assumptions that were incorrect.
- Fixed a bug where on some Perl installations the timeout would not be caught and handled correctly.
- SpaMo
- Corrected a link to an example motif file on the job submission form.
- Tomtom
- Fixed bug in Tomtom's pearson_scores(): replaced integer division with floating point.
- Other
- When sequences are skipped due to a duplicate name the warning message is not generic anymore.
- Replaced broken link to old user forum with link to new Q&A site.
- Removed non-functional -P switch from ceqlogo. Use "-d ''" to supress fineprint.
- Added documentation of "--uniform--" keyword for "--bgfile" switch.
- Updated source for Eukaryotic Promoter Database (listed in etc/db_general.csv).
- Fixed a bug where the release date was being truncated by some older programs in the MEME Suite.
- Fixed usage message of create-priors.
MEME version 4.9.0 patch 4 -- January 18, 2013
- New Features and Enhancements
- CentriMo
- Added computation of p-value ratio whenever
negative sequences are given. The p-value ratio
seems to be more useful than the discriminative
p-value computed in the
--disc
mode,
and is much faster to compute. Motifs are now sorted by
p-value ratio by default when negative sequences
are given and --disc
is not.
- Added feature to supress plotting of negative sequence
enrichment curves so a single run can be used for
comparative and absolute enrichment analysis.
- Sorting on Region Center now sorts by increasing
absolute value (centrality) of the location of the region.
- The "region" sorting feature menu is now locked to the
same value as the "motifs" feature menu, unless a checkbox
is checked. This helps prevent confusion.
- Improved documentation popups.
- Fixed bug in the Fisher's Exact test (affected AME,
too).
- Added new standalone utility: fisher_exact
- MEME-ChIP
- Added -centrimo-local switch to allow CentriMo to perform
local motif enrichment as part of MEME-ChIP.
- FIMO
- Added
--parse-genomic-coords
option.
This option turns on parsing of UCSC style genomic
coordinates from sequence headers.
- taipale2meme
- Add options [-nc ]+ and [-oc ] to accommodate
format of Jolma2013 Cell paper.
-
Bug fixes
- Fixed buffer overflow bug in shift_sequence().
- Fixed bug in DREME: -norc option resulted in incorrect PSSM.
MEME version 4.9.0 -- October 2, 2012
- New Features and Enhancements
- CentriMo
- Added local mode for detecting uncentered enriched
regions.
- Added discriminative mode which takes two datasets
and uses the Fisher's exact test to detect discriminatively
enriched regions.
- Added listing of sequence IDs in output for best
enriched regions.
- Added score threshold optimization mode.
- Updated website form to give access to local mode and
discriminative mode.
- FIMO
- Simplified command line options controlling output threshold.
- FIMO no longer emits a wiggle format file.
The wiggle file contained the same information as the GFF file,
but was more verbose.
- Output of '--text' option now matches format of 'fimo.txt' file.
- Text file now provides explicit strand information.
- Text file now lists start and stop coordinates in increasing order relative to the positive strand
for all matches.
- HTML output is now limited to the 1000 most significant matches.
- MEME-ChIP
- Complete rewrite of the MEME-ChIP program to run MEME,
DREME, Tomtom and CentriMo.
- New output which collates all the motifs found by the
called programs with links to their outputs.
- New website form allows choice of motif database and
adds more options for DREME and CentriMo.
- Tomtom
- Creation of EPS and PNG Logo files is now optional to
save disk space.
Two new switches (-png and -eps) have been added to the
command line version of Tomtom.
- meme-rename
- Added new script meme-rename for mass renaming of
output html files so they can inhabit the same directory.
- psp-gen
- Added handling of ambiguous IUPAC alphabet
symbols for DNA bases.
- New Motif Databases
- Malaria transcription factor motifs from PBM experiments
(Campbell et al., 2010 PLos Pathogens)
- New motifs derived from the original UniPROBE PBM data using
a different algorithm (Zhao and Stormo,
2011 Nature Biotechnology)
-
Bug fixes
- Fixed FIMO bug--nucleotide motifs were labeled as polypeptide motifs in GFF output
- Fixed FIMO bug--both motifs and RC motifs were printing in list of best possible matches
- Fixed CentriMo bug--"--motif" option was not functional.
- Fixed bug in gendb--was failing with higher-order models.
- Fixed bug in gendb--was failing with higher-order models.
- Updated the MEME installation guide
- Removed unused documents
MEME version 4.8.1 -- February 6, 2012
- New Features and Enhancements
CentriMo
- Added method to create custom Encapsulated Postscript
files of the motif probability graph.
MEME-ChIP
- Added SpaMo to the list of programs that MEME-ChIP
runs.
- Bug fixes
- Fixed a typo which was breaking the "Upload your own
database" feature on Tomtom.
MEME version 4.8.0 -- January 16, 2012
- New Features and Enhancements
CentriMo
- Added HTML output with lots of interactive features
allowing selecting, sorting and filtering of which motifs to
display and plot the site-probability curves for.
- Added
CentriMo
web submission form.
CentriMo
now runs as part of MEME-ChIP
.
- Can now use motif matches to the given strand only if the
-norc
switch is given. Useful with RNA sequences.
- Removed
centrimo-plots
program as the new
HTML output replaces and improves on its purpose.
DREME
- Can now look for motifs on the given strand only if the
-norc
switch is given. This can be useful with
RNA sequences.
- Using given strand only now available as an option on the web
submission form.
MCAST
- Added support for scanning genome scale sequences.
- Added q-values for match scores.
- Revised HTML output to include block diagrams of matches.
SpaMo
- SpaMo now normalizes the p-values reported for particular
motif spacings (bins) only for the number of spacings (bins)
tested. Previously, SpaMo reported p-values normalized for
both the number of spacings and the number of motifs tested.
- SpaMo now prints E-values for secondary motifs, which is the
lowest p-value of any spacing (bin) times the number of secondary
motifs.
- Added -evalue switch to specify largest E-value allowed for
secondary motifs.
- Other
- Improved memory efficiency for reading FASTA sequences in sequence.py.
- Bug fixes
- Fixed segmentation fault in FIMO when option
--bgfile motif-file
is used.
- Fixed png generation code for custom motif logos.
MEME version 4.7.0 -- September 22, 2011
- New Features and Enhancements
- DREME can be accessed as a webservice directly which
allows use of the discriminative motif discovery.
- DREME now produces XML and HTML outputs as well as text.
These new outputs are accepted where MEME motifs are
accepted.
- New command-line program
CentriMo and the associated
CentriMo Plots for
determining which motifs are centrally enriched in ChIP-seq
output.
- Completely rewrote motif loading code. The main user
visible difference is that the minimal MEME format is a
lot more forgiving of spacing and MAST can now accept the
minimal MEME format without any PSSM section.
- Output from all tools now lists the preferred citation.
- Updated and re-formatted list of publications.
- Bug fixes
- Occasionally MEME would produce HTML files which could not
be used as a motif input to other programs. The new motif
parser should be able to read these files and hence fix this
problem.
- SpaMo background is now calculated from the sequences as
stated in the paper.
- The website menu used to use the full URL which
unfortunately resulted in people bookmarking specific versions
of the MEME suite rather than the URL for the latest version.
The website menu has been corrected to use only relative
URLs.
- Links should now be created to the error messages when
a webservice fails. This used to work but some setting changed
the way redirects are buffered.
- Added compiler/linker directives to set stack size for
Cygwin to 9MB. Cygwin defaults to a 2MB stack, which is too
small.
- MAST was not handling the
-remcorr
switch.
When a motif was removed because it was too correlated, the
indices of the other motifs could be incorrect. Fixed.
- Known issues
- DREME does not yet support single strand scanning. It is
planned but wasn't ready for this release.
- Uploading extremely large sequence sets to MEME-ChIP can
cause a HTTP timeout and/or failure of the CGI script.
MEME version 4.6.1 -- March 21, 2011
- New Features and Enhancements
-
MEME-ChIP
command line tool --
MEME-ChIP was released in 4.6.0 as a web service but it did not
have a command line equivalent. The webservice has been rewritten
as a command line tool.
-
Tomtom
--
The default Tomtom scoring algorithm now considers all columns in the
query motif, not just the aligned columns. This reduces the
number of spurious alignments including uninformative columns.
The older scoring system is available via the
-incomplete-scores
option.
- Bug fixes
-
MEME-ChIP
--
-
MEME-ChIP has been rewritten to avoid infinite loops that
could occur when the webservice was passed parameters including
colons.
-
The webservice now updates its output with the
completion of each sub-program so if it is terminated by Opal
for running too long the already completed output is still available.
-
Error reporting has been improved with the result that
MEME-ChIP should not be able to fail mysteriously as it has
on occasion been doing.
-
FIMO
-
The
--norc
option was being ignored.
This has been fixed.
-
Motiph
-
The
--seed
option has been added to set the
seed for the random number generator.
- Known issues
- MEME-ChIP when given very large sequence sets will not complete before the Opal webservice time limit.
- Uploading extremely large sequence sets to MEME-ChIP can cause a HTTP timeout and/or failure of the CGI script.
MEME version 4.6.0 -- December 24, 2010
- New Features and Enhancements
-
MEME-ChIP
web service --
- Motif Analysis of Large DNA Datasets
The MEME-ChIP service allows submission of a FASTA file of DNA sequences
of unlimited size and with minimal parameter settings (only the traditional
MEME web form settings) and runs it through a variety of motif finding and
analysis tools.
-
dreme
--
added dreme
and integrated it into the MEME-ChIP into web service.
-
AME
--
added ame
and integrated it into the MEME-ChIP into web service. This
is a cut-down version of the ame
previously described, only supporting one mode
of motif enrichment analysis.
-
fasta-dinucleotide-shuffle
--
added scripts/fasta-dinucleotide-shuffle
and integrated it into the MEME-ChIP into web service.
Thanks to Peter Clote for allowing use of his dinucleotide shuffle code.
-
fasta-center
--
added fasta-center
and integrated it into the MEME-ChIP into web service.
-
SpaMo
beta release --
The web interface and documentation is currently rather limited but in the interests of
getting this out for review this is a preview edition of the Spaced Motif analysis tool.
-
FIMO
--
The FIMO
HTML output now explicitly labels the strand,
rather than indicating the reverse strand by having start
> than stop
.
The HTML output also now includes the matched sequence.
The GFF output is now GFF 3.
MEME version 4.5.0 -- September 6, 2010
- New Features and Enhancements
-
Tomtom
--
- Search multiple databases
Tomtom can now search more than one motif database.
To keep the ability to have web links for each motif
they were moved into the MEME motif format itself.
See the documentation.
- Improvements in submission form
Tomtom's submission form has many new enhancements.
Motifs can now be specified in 3 formats: IUPAC motifs,
frequency matrices, and MEME format files.
Go try it.
- Improvements in output format
Tomtom now outputs an XML file which it converts into
the HTML output. The HTML output can dynamically
draw the motif logos when the images aren't available
on web browsers supporting HTML5. Additional improvements
include a summary table at the top giving direct links to the
top 20 matches for each motif. See the
sample.
FIMO
--
The output for FIMO now includes a
wiggle track format file.
- MEME file format --
The MEME file format now includes an optional URL for each motif. This is used
to create the links in the Tomtom output. All the XXXX2meme scripts have been
retrofitted to take this URL parameter.
-
ama-qvalues
--
New script. See the documentation.
-
fasta-subsample
--
New script for extracting a random sampling of the sequences
in a FASTA file. This is especially useful for ChIP-seq
peak datasets to be input to MEME. Using this script, a
FASTA file containing a subset of the ChIP-seq peak sequences
(or any other FASTA file) can be created. The total
number of sequences should be less than 1000 (preferably less
than 500), and the total sequence length should be less
than a few hundred thousand. MEME typically takes about 20 minutes
per motif with files of 100,000 characters (DNA, both strands, ZOOPS model),
and scales quadratically in the total sequence length (so a file of
200,000 characters will take four times as long.)
This new script can also output the remaining sequences (in a separate
file) for use in cross-validation. See the documentation.
-
meme2meme
--
New script. See the documentation.
-
rna2meme
--
New script. See the documentation.
MEME version 4.4.0 -- April 23, 2010
- New Features and Enhancements
-
MCAST
--
MCAST
now been integrated into the MEME Suite web applications.
MCAST is a tool for searching for
statistically significant clusters of motifs in DNA sequences.
MCAST was previously supported on a separate web site.
-
MEME
- Discriminative motif discovery
The MEME web server now supports discriminative
motif discovery. The user may now provide a set
of "negative sequences" in addition to the normal
"positive sequences", and MEME will look for
motifs that are overrepresented in the positive sequences
relative to the negative sequences.
- Improvements in output format
MEME's html output (sample) has been reorganized to
make important information more accessible as well as to make it aesthetically pleasing. Some of the improvements
include:
-
A preview of the motifs found, including their reverse complement for DNA, in miniature at the top of the page.
-
Ability to view full sized reverse-complemented DNA logos.
-
Highlighting of all output for a sequence with a single click.
-
New block diagrams that graphically show the strength (and DNA strand) of motifs,
and that scale with the size of the browser window.
-
Support for the new web standard HTML5. This allows the motif logos to be viewed without the images
on supporting web browsers (Firefox, Chrome, Safari). Unfortunately Opera has inadequate text support for canvas
(the new HTML5 element required for this feat) and Internet Explorer currently doesn't support canvas at all.
It is anticipated that Internet Explorer 9 will support this feature.
-
MAST
--
- Improvements in output format
MAST's html output (sample) has been reorganized to
make important information more accessible as well as to make it aesthetically pleasing. Some of the improvements
include:
-
Everything is now in one place - no longer do you have to search to find the associated annotated sequence for that
high scoring sequence, as with one click the hidden information is displayed directly below. Additionally if DNA
strands are scored separately then the sequence only appears in the list once based on the better scoring strand.
-
New block diagrams - incorporating all the improvements in the new MEME block diagrams such as graphical display of
motif strength, scaling with the browser window and the DNA strand. As an added bonus separately scored strands
are visible on the same diagram.
-
Interactive annotated sequence - a new range selector allows you to view the sequence around the motif hits of your
choice, directly relatable to the block diagram. For separate DNA strand scoring only one strand is visible at a time.
-
Now in colour - the annotated sequence for motif hits now have letters colour coded using the same colour scheme
as MEME motifs.
- MAST now outputs xml in a similar fashion to MEME. This has resulted in differences to how you would invoke MAST
from the command line. Additionally it no longer has the script wrapper.
- MAST now uses an xml style sheet to create its html output.
-
mast2txt
--
Created program mast2txt for outputting the old text format for MAST. Note that there are some
problems with backwards compatibility in separate scoring mode. The use of the text format is no longer recommended.
-
psp-gen
--
added psp-gen
and integrated PSP generation into web service.
-
MHMM
--
Fixed bug in --order
option.
The option was handling motifs with strand identifiers incorrectly.
Tomtom
--
Added -no-ssc
switch to fix problem with
motifs with few sites having empty logos; this switch is now
the default for the Tomtom website.
GOMO
--
Improved gomo html format.
Added highlighting of the most specific GO terms in
the html output. This is activated by the switch --dag
which expects a GO DAG file.
gomo_highlight
--
Added a program to post process gomo xml files to
identify the go terms which are implied by other
more specific go terms to allow the specific terms
to be highlighted in the html output. This is used
by gomo when the --dag switch is specified.
-
obo2dag
--
Added a tool for generating a GO DAG file from a
Gene Ontology OBO file.
-
GO DAG format
--
Documented the new GO DAG file format and improved GOMO
documentation as well as the command line overview.
-
GLAM2
--
The output now prints a regular expression in addition to the logo
for each motif found.
-
MEME motif format
--
Fixed errors in motif format description
doc/meme-format.html
and example files.
-
meme-io
--
Updated meme-io to accept the new MEME html format.
MEME version 4.3.0 -- September 26, 2009
- GOMO --
Added comparative genomics to GOMO. GOMO can now use
multiple, comparative genomes in making its predictions.
This substantially increases the sensitivity of predictions of roles
for DNA binding motifs. The GOMO web-service now
uses GC-compensated AMA p-values.
- AMA --
P-values are no longer printed by default. A switch
has been added to cause them to be printed.
AMA can now compute GC-content compensated p-values.
The GC-content of an individual sequence is used in estimating
the p-value of its AMA score.
MEME version 4.2.0 -- June 22, 2009
- MEME --
MEME now can use position-specific priors (PSP) to improve
motif discovery. The PSP is specified using the
-psp pspfile
switch to MEME.
- GOMO --
Added the ability to choose either maximum or average
binding affinity as the scoring function.
Fixed a bug--was using
maximum affinity by default, contrary to the documentation.
- AMA --
AMA now computes p-value of each sequence based on
a 0-order background model for the dataset.
Improved speed and memory efficiency; was re-reading sequences
and storing them in memory.
Fixed bug--was using max-odds by default
and the --scoring switch was being ignored.
- MAST -- website now supports protein databases even when
DNA database contains long sequences.
- Installation --
Now all programs in the MEME suite are built.
The --enable-both configure switch is now obsolete.
Simplified the build process by removing support for separately building
the tools formerly included in Meta-MEME.
Update on-line documentation.
Simplified "quick install" instructions are provided in INSTALL
and in doc/meme-install.html
.
MEME version 4.1.1
- Improved documentation.
- Increased default number of iterations for GLAM2.
- Improved error handling for sequence data.
- Added links to server activity summary.
- Fixed bug in install process when
--enable-both
not used.
MEME version 4.1.0
- New tool: GOMO -- Finding Genome Ontology terms associated with
DNA binding motifs.
- Added FIMO and GOMO buttons to MEME output to make it
easy to use discovered motifs to search sequence databases
and to identify the role of DNA binding motifs.
- Fixed placement of sidebar menu in Internet Explorer for output of CGI scripts.
- Fixed support for OpenMPI in MEME.
- Improved the efficiency of FIMO.
-
Made the
-text
option to FIMO produce results on-the-fly,
without sorting or q-values. This mode allows very large databases to
be searched, without storing intermediate results.
-
Modified the command line syntax for
gendb
, for
consistency with the rest of the suite.
MEME version 4.0.0 -- June 13, 2008
- New Features and Enhancements
- MEME and Meta-MEME are now integrated as "The MEME Suite".
- New web-based tools:
- GLAM2 and GLAM2SCAN--discovery and scanning of gapped motifs
- Tomtom--comparing motifs
- FIMO--basic motif scanning (complements MAST)
- Enhancements of existing tools:
- Sequence LOGOS now enhance MEME output.
- Compare new motifs to databases of motifs
via Tomtom by clicking an easy-to-use button on MEME and GLAM2
output.
- Improved local search (branching search) in MEME
(command line version only).
- Hundreds of new genomic and upstream sequence databases
are now supported for scanning by MAST, FIMO or GLAM2SCAN.
- Tomtom supports four motif databases: JASPAR, Transfac, SCPD
and MacIsaac Yeast.
- The MEME Suite tools now have web servers powered by OPAL,
and return their results via the web, rather than by email.
- A single web server portal simplifies
different types of motif scanning tasks
MEME version 3.5.7 -- December 14, 2007
- New Features and Enhancements
- Parallel MEME is compiled when no scheduler is found but MPICH is detected.
- Opal integration with meme.
- Added --enable-webservice=<path_to_build-opal.xml> configure flag.
Used to automate deployment of MEME inside an Opal installation as a web service.
- Added --enable-web=<opal_url> configure flag.
Used to enable building of the MEME web portal.
A URL for an Opal-exposed MEME web service must be entered.
MEME version 3.5.5 -- May 31, 2007
- New Features and Enhancements
- MAST -hit_list can now handle very long sequences
and prints ALL hits regardless of the sequence E-value cutoff.
It splits them into "swaths". The -hit_list switch now
overrides the -seqp switch, and hits are NOT sorted
by the E-value of the sequence.
MEME version 3.5.4 -- September 21, 2006
- New Features and Enhancements
- Bug fixes
- Fixed printing of command name in MAST results.
- Fixed the handling of the "View FASTA", "View RAW" and "View motif summary"
buttons on the MEME form.
- Improved documentation of the "Motif Summary" section of MEME output.
- Fixed bug that prevented having multiple MEME and MAST servers running on a
single host by different users. Each server is distinguished by the socket number
it listens on.
- Known Issues
- The "MetaMEME" button on the top of MEME results page is still not functional.
Users are advised to go to the MetaMEME web site and submit manually at this time.
- MAST: Uploaded file names containing quotation marks may cause the search to
fail.
- MAST: Uploaded sequences in DOS/Windows format may cause the search to fail.
MEME version 3.5.3 -- April 20, 2006
- New Features and Enhancements
- The capability to search three JASPAR databases of DNA motifs
for matches to a MEME-discovered motif has been added to the MEME
output form. Pressing the 'COMPARE PSPM' button on the results
form of a MEME search of DNA sequences will submit the selected
motif PSPM to the JASPAR 'Compare' server. This will allow you
to determine if your motif is similar to any known motifs contained
in one of the three JASPAR motif databases.
- Bug fixes
- The "MAST" button on the top of MEME results page now automatically loads the
motifs from the MEME results for MAST search. A user only needs to choose the database
(uploaded or server side) to search against.
MEME version 3.5.2 -- March 1, 2006
- New Features and Enhancements
- Newly designed web interface using javascript and css styling.
- Add support for Macos X server startup.
- Add meme-install.html with detailed explanation of installation
procedures.
- Bug fixes
- In "configure" remove check dependency on parallel condition when
creating server executables.
- Path to images/ in cgi scripts.
- Description syntax in linux startup script meme.linux.
- Provide fix for a cygwin's new line representation when searching strings.
- Bug in e_step (oops.c)
- Bug caused by typo "MEME_BINbin"
- Remove use of min() in meme.pl
- Remove obsolete argument sample_prob from subseq7()
- Remove OS-dependent declarations of accept(), bind(), connect(),
socket(), listen(), htons(). They are defined in system header files.
MEME version 3.5.1 -- December 15, 2005
-
Bug fixes
- Revert binary and scripts names to what they used to be in version prior to 3.5.0.
The binary executables have an extension ".bin", and the shell scripts have
their extension ".csh" removed. This allows to keep compatibility with
earlier versions.
- Change startup scripts to start servers as a user specified during configuration.
If none were specified, then the uid of the user who runs configure will be
used.
- Always install files in etc/.
- Always install Globals.pm in lib/perl/.
- Move meme-explanation.html from web/html/ to etc/. This allows to run scripts that do
conversion to html when web site is not installed.
-
Enhancements
- Added support for Macos X (serial version only, without server)
- Users can now compare DNA motifs to the motifs in the JASPAR database of transcription
factor binding site motifs. A button is provided in the PSPM section of each DNA motif
on the MEME output form for this purpose. Clicking on the "Compare PSPM x to known motifs
in JASPAR database" sends the motif to the JASPAR website, which returns any similar motifs
that are found.
- Add meme_config.csh file that is used automatically by csh scripts to set
needed environment variables.
- Move job.out file (created when SGE scheduler is used) to LOGS/
- Add '--with-serial' option to 'configure.ac' for compiling only serial
version
- Disable installation of web by default. To install use --with-web configure
option.
- Lower prerequisite version for autoconf to 2.53, and add missing functions in m4/.
Add check for autoconf version in bootstrap, and use m4 functions when
needed.
- Change option '--with-mpi' to '--with-mpidir'
MEME version 3.5.0 -- September 15, 2005
This is the 12th year of MEME development. The current anniversary
maintenance release
for MEME contains a number of improvements to the installation and configuration of MEME/MAST
servers and clients. Thanks to Nadya Williams of SDSC/NBCR for this work.
-
Refactoring of installation and configuration
- Restructure source directory tree to ease configuration.
- Highly simplified and optimized installation and configuration for MEME and MAST servers
and clients using GNU autoconf/automake tools.
- Multiple configuration options available via arguments to "configure".
- Default installation of MEME, MAST server and clients, as well as the web
site.
- Separate installation of server, client or web site if desired.
- Create a small test suite for 'make test'.
- Implement procedures for standard 'configure', 'make', 'make test', and 'make
install'.
- Create scripts to run MEME/MAST servers as services, and automatically restarted them
when physical host server reboots. Currently, Linux and SunOS are supported.
- Simplified start of the servers with 'start-mast' and 'start-meme' scripts.
- Encapsulate site-specific variables in Globals.pm for perl scripts
and in meme_config for sh scripts.
- Add csh and sh configuration scripts to set working environment.
- Availability as a Rocks Roll for integration with
Rocks based cluster system.
-
Enhancements
- Sent MEME/MAST search results via an email as attachments, rather than inlined in the
message body. This allows the MEME output to be saved properly for subsequent
use with MetaMEME. It also reduces the chance of the output being modified by email
filters.
- Check email addresses for entry accuracy using javascript. Thanks to Chris
Misleh of NBCR for this feature.
- Check email addresses for valid domain names.
- Create new 'runtests' script to run all test suites. Simplify parsing of the
output.
- Update FAQ(s) for MEME and MAST.
- Separate web-related files by type (html, cgi or image) and create a dir structure
to support it. This simplifies web maintenance.
- Add examples of database and motif sequences files.
-
Known Issues
-
Support Team Members
Wilfred W. Li, Ph.D., Nadya Williams, M.S., Chris Misleh, and Timothy Bailey, Ph.D.
MEME version 3.0.14 -- July, 2005
-
Bug Fixes
-
an array out of bound error when MEME is run in parallel mode using certain DNA
sequences with the "look for palindromes only" option enabled. Thanks to Tim Kaiser of
SDSC/NBCR for the bug fix.
-
User Support
- all user questions are directed to our support team<EMAIL_ADDRESS>MEME version 3.0 -- December, 2000
-
MEME enhancements
-
Hypertext output: MEME now reports its output in hypertext (HTML)
format with appropriate internal hot links among the results and the
self-contained documentation on how to interpret them. The
alignments are color-coded by nucleic acid or amino acid category.
-
Direct MAST search: MEME motifs can now be used to search
sequence databases using MAST simply by clicking on a button on the
MEME HTML output document in an HTML-capable email reader or browser.
-
Direct BLOCKS search: MEME motifs can now be submitted to the
BLOCKS multiple alignment processor by clicking on a button on
the MEME HTML output document in an HTML-capable email reader or
browser. This allows MEME motifs to be converted to LOGOS or trees,
and to be used to search other databases of motifs.
-
New objective function: MEME searches for motifs that optimize
the statistical significance of the log likelihood ratio of the
occurrences of the motif.
-
E-values: MEME computes and reports the statistical significance
of motifs as the E-value of the log likelihood ratio. This provides
an objective measure of how likely the motif is to be biologically
significant.
-
E-value stopping criterion: MEME will now stop when a motif
whose E-value is above a user-given threshold is found. This guarantees
that only motifs with a given E-value or better will be present in the
output.
-
Handling reverse complement DNA strands: MEME now handles
reverse complement DNA strands correctly with all model types:
OOPS, ZOOPS and TCM.
-
Handling of ambiguous characters: MEME now handles ambiguous
DNA and protein letters by converting them to the character "X".
MEME treats the "X" character as "unknown", and correctly computes
the probabilities of motif occurrences containing it.
-
Higher-order background models: MEME now allows the user to
specify a Markov model of arbitrary order via a file of tuple
frequencies. This appears to improve the ability to discriminate
between biologically interesting DNA motifs and motifs that are
artifacts of the higher order statistics of DNA sequence.
-
Multiple-alignment-based motif trimming:
MEME defines a motif as
a set of subsequences that can be correctly aligned without gaps.
MEME can now trim
the edges of motifs based on a local multiple alignment with gaps. MEME
first determines the occurrences of the motif, then aligns each
occurrence to the highest-scoring occurrence. These are combined
into a multiple alignment, and MEME looks for a set of columns with
no gaps. If a set of gapless columns at least <minw> wide is not
found, MEME searches for a set with at most 1, 2, ... etc gaps until
a set is found.
-
Prior distribution on the number of occurrences: MEME now
places a prior on the number of occurrences that controls how
strong the bias towards motifs with a given number of sites is.
Using a prior improves the performance of MEME with DNA, where the
megaprior heuristic (used by default with protein sequences),
is not applicable.
-
MAST enhancements
-
Combining DNA strands: MAST now combines the score of a
site in a DNA sequence with the score of the corresponding site
on the reverse complement strand. (The final score for the site
is the maximum of the two scores.)
-
Scoring DNA strands separately: MAST still allows each strand
of a DNA sequence to be treated as a separate sequence at the
user's request.
-
Ignoring reverse complement DNA: MAST also allows the user to
score only the given DNA strand, not scoring the reverse complement
strand at all.
-
Background model: MAST now allows the user to specify the
background residue frequencies used for computing E-values of scores.
-
Composition-adjusted statistics: MAST can now use a different
random model for each target sequence, based on the letter composition
of that sequence. This can greatly reduce erroneous matches due
to biased sequence composition.
-
New databases:
The MAST website includes several new databases including "upstream"
sequences for E. coli, B. subtilis and S. cerevesiae, and many complete
genomes from GenBank.
-
MEME and MAST enhancements
-
MEME and MAST can be installed under the following operating systems:
- Mac OS X
- Linux (various manufacturers)
- SunSparc workstations (SunOS and Solaris operating systems)
- Decalpha workstations (OSF/1 operating system)
- Silicon Graphics workstations (IRIX version 5.3 operating system)
- Intel Paragon parallel computers
- Cray T3D parallel computers
- IBM SP (AIX operating system)
MEME version 2.2 -- February 25, 1998
-
MEME enhancements
- Sequence weights can be given in the input sequence file.
-
The sites composing each motif are output in BLOCKS or FASTA format.
BLOCKS format motifs can be converted to LOGOS, PSSMS and phylogeny trees
using the
Blocks Multiple Alignment Processor.
-
A "negative" dataset may be specified causing the motifs to be optimized
to discriminate between the training set family and the negative family.
(This option is only available when you install MEME on your own computer.)
-
An advanced version of the MEME data submission form allows
- discovering palindromic DNA motifs,
- discovering motifs occurring on both DNA strands, and
- discovering more than ten motifs.
-
MAST enhancements
-
DNA sequences (translated in six reading frames) can be searched
using protein motifs.
-
Hypertext (HTML) output
including links to the ENTREZ database and
improved motif diagrams are now output.
- Additional searchable databases added to the MAST website.
-
The annotation section of output is smaller now since only
regions in sequences where the motifs are present are printed.
-
The ambiguous characters "*" and "-" are now permitted in motifs
and sequence databases. They are treated as a single, unknown
character in databases, and replaced by a weighted average of
scores in motifs.
MEME version 2.1 -- March 25, 1997
-
Enhancements
- MAST output now includes measurements of similarities between
all pairs of motifs in the query and a warning if any motifs
are too similar. (Too similar motifs in a query can cause
some p-values and e-values to be underestimated. These motifs
can be removed from the query and MAST re-run to avoid the problem.)
- Cray T3E parallel computer now supported for MEME and MAST.
MEME version 2.0 -- October 17, 1996
-
Enhancements
-
The output format of MEME has been
improved to aid readability and user-friendliness.
-
MEME and MAST have been compiled and tested on:
- SunSparc workstations (SunOS and Solaris operating systems)
- Decalpha workstations (OSF/1 operating system)
- Silicon Graphics workstations (IRIX version 5.3 operating system)
- Intel Paragon parallel computers
- Cray T3D parallel computers
-
MAST has been completely rewritten to provide more accurate
p-values and to run significantly faster.
- A MAST server has been added to the MEME system website.
-
The MAST server lets you use the motifs found by MEME in your sequences
to search a wide variety of sequence databases including:
- nr (non-redundant protein and nucleotide databases)
- month (new or revised sequences in the last 30 days)
-
swissprot (the last major release of the SWISS-PROT protein sequence
database)
- genpept (protein translations from the GenBank feature table)
- dbest (expressed sequence tag database)
- dbsts (sequence tag site database)
- Several improvements have been made to the MEME website:
-
You can now give the name of a file containing your sequences
instead of having to cut-and-paste the sequences themselves.
-
You may ask MEME to favor wide motifs instead of the (default) narrow
motifs; this is especially useful with small sequence sets (fewer than
10 sequences.)
- The on-line documentation of MEME has been expanded and improved.
-
MEME now determines the type of your sequences
(PROTEIN or DNA) automatically.
-
The MEME server now runs MAST on your sequences to make it easy for you
to see the ordering and spacing of the motifs MEME discovered.
-
NOTE and PROBER have been removed from the MEME system since their
functionality is now superseded by MAST.
MEME version 1.4 -- February 29, 1996
-
Megaprior heuristic added to MEME.
-
MEME now uses the megaprior heuristic with TCM models and the modified
megaprior heuristic with ZOOPS models (by default). This greatly improves
the sensitivity and selectivity of motifs using these types of models.
-
P-value computation added to MAST.
-
MAST now computes p-values for sequences when searching large databases.
This provides better discrimination between true and false positives than
using z-scores. MAST is still only available via ftp, not via the web server.
- Various bug fixes to MEME.
MEME version 1.3 -- December 18, 1995
- MEME web server introduced!
- Various bug fixes to MEME.
MEME version 1.2 -- November 27, 1995
- MAST homology searcher introduced!
-
MAST allows accurate homology searches of databases using motifs generated
by MEME. The scores from all motifs characterizing a family are combined,
normalized for sequence length, and sorted by z-score. The output of MAST
is similar to that of BLAST, but, used in conjunction with MEME, MAST
allows searching for sequences related to an entire family, not just a
single sequence in the family. This provides better sensitivity and
selectivity than single-sequence homology searches.
MAST is currently only available in the ftp-able code, not via the web server.
- Various bug fixes to MEME.
MEME version 1.1 -- June 30, 1995
- Initial release of MEME, NOTE and PROBER.
Meta-MEME Release Notes
Release 3.3
-
The program
motif-scan
has been renamed to
fimo
Release 3.x, Release 3.3, March 24, 2007
-
Added new tools:
-
motif-scan
-
Scans a database of sequences for the presence of motifs by
calculating the p-value of the match to the motif at each position
in the sequences.
-
shadow
-
Calculates the log-odds of a multiple alignment for a given phylogentic
tree and evolutionary model at each position in the alignment.
-
motiph
-
Scans a multiple alignment for the presence of motifs by
by calculating the p-values of motif-width windows in the alignment
for a given phylogentic tree and evolutionary model.
-
tom-tom
-
Searches target motifs for elements similar to any in a set of query motifs.
-
Added
--global
option to mhmms
.
This option causes mhmms
to score sequences using the best
match between the model and the entire sequence.
The default is to score using the best local match within a sequence.
-
Added
--maxhits
option to mhmms
.
This option sets an absolute limit to the number of hits
returned by mhmms
.
The default is to return all hits consistent with the
E-value and p-value thresholds.
-
Fixed error in
mhmms
that resulted in a sequence being considered
a hit even if all positions were matched to a spacer state.
-
Fixed error causing segmentation a fault in
mhmms
when the
--motif-scoring
or --pthresh
options were used.
-
Fixed error causing segmentation a fault in
mhmm
when the
--order
option was used.
Release 3.21, August 3, 2005
- Modified meme-io.c to be able to parse the output from the latest versions of MEME.
-
Modified the mcast script: removed the -allow-weak-motifs swich, and added the --keep-unused switch
to the call to mhmm from mcast.
Release 3.2, October 7. 2004
- Reorganized source directory structure and implemented build
system using autoconf and automake.
- Updated program documentation.
Release 3.1, February 4, 2004
- Remove the auxiliary program
score-n-store
.
- Change command-line processing to follow POSIX.2 standard.
Release 3.0.1, June 2, 2003
- Add documentation for MCAST.
Release 3.0, May 15, 2003
- Remove
mhmmt
(EM training program) and
mhmma
(multiple alignment program).
- Add
mhmmscan
and the mcast
wrapper
program for searching DNA databases for regulatory modules.
- Allow star topology in
mhmm
.


To see the LRFP document, click in the hyperlinked text in the LRFP field.
In the header of the record, you will see the school district the LRFP is associated to.


React Sparklines
Beautiful and expressive sparklines component for React
View on GitHub
npm install react-sparklines
Simple
Simple Curve
Customizable
Spots
Bounds
Bars
Dynamic
Reference Line
Normal Band
Real world examples


Welcome to pythologist-image-utilities’s documentation!¶
Readme File¶
pythologist-image-utilities¶
For function details please Read The Docs
Functions for working with image data in python
About¶
This set of functions are used in the construction of pythologist-reader intermediate storage format, and in the analysis of image data .. finding neighbors .. or the generation of images.
Modules¶
-
pythologist_image_utilities.
binary_image_dilation
(np_array, steps=1)[source]¶ For an input image that gets set to 0 or 1, expand the 1’s by the number of steps
- Parameters
np_array (numpy.array) – a 2d image
steps (int) – number of pixels to expand
- Returns
Image with that has been expanded
- Return type
numpy.array
-
pythologist_image_utilities.
flood_fill
(image, x, y, exit_criteria, max_depth=1000, recursion=0, visited=None, border_trim=1)[source]¶ There is a flood_fill in scikit-image 0.15.dev0, but it is not faster than this for this application. It may be good to revisit skikit’s implemention if it is optimized.
- Parameters
image (numpy.array) – a 2d numpy array image
x (int) – x starting coordinate
y (int) – y starting coordinate
exit_criteria (function) – a function for which to exit i.e.
lambda x: x!=0
max_depth (int) – a maximum recurssion depth
recursion (int) – not set by user, used to keep track of recursion depth
visited (list) – list of (x,y) tuple representing coordinates that have been visited
border_trim (int) – the size of the border to avoid on the edge
- Returns
the filled image
- Return type
numpy.array
-
pythologist_image_utilities.
image_edges
(image, verbose=False)[source]¶ Take an image of cells where pixel intensitiy integer values represent cell ids (fully filled-in) and return just the edges
- Parameters
image (numpy.array) – A 2d numpy array of integers coding for cell IDs
verbose (bool) – If true output more details to stderr
- Returns
an output image of just edges
- Return type
numpy.array
-
pythologist_image_utilities.
make_binary_image_array
(np_array)[source]¶ Make a binary (one channel) image from a drawn color image
- Parameters
np_array (numpy.array) –
- Returns
an array that is 1 where something (anything) existed vs 0 where there was nothing
- Return type
numpy.array
-
pythologist_image_utilities.
map_image_ids
(image, remove_zero=True)[source]¶ Convert an image into a list of coordinates and the id (coded by pixel integer value)
- Parameters
image (numpy.array) – A numpy 2d array with the integer values representing cell IDs
remove_zero (bool) – If True (default), remove all zero pixels
- Returns
A pandas dataframe with columns shaped as <x><y><id>
- Return type
pandas.DataFrame
-
pythologist_image_utilities.
median_id_coordinates
(np_array, exclude_points=None)[source]¶ Locate a coordinate near the center of each object in an image
- Parameters
np_array (numpy.array) – Take an image where pixels code for the IDs
exclude_points (list) – optional. a list of tuples of ‘x’,’y’ coordinates. to exclude from being possible median outputs
- Returns
DataFrame indexed by ID with a near median ‘x’, and median ‘y’ for that ID
- Return type
pandas.DataFrame
-
pythologist_image_utilities.
read_tiff_stack
(filename)[source]¶ Read in a tiff filestack into individual images and their metadata
-
pythologist_image_utilities.
watershed_image
(np_array, starting_points, valid_target_points, steps=1, border=1)[source]¶ A function for expanding a set of pixels in an image from starting_points and into valid_target_points.
- Parameters
np_array (numpy.array) – A 2d array of the image where comprised of integer values
starting_points (list) – a list of (x,y) tuples to begin filling out from. the values of these points
valid_target_points (list) – a list of (x,y) tuples of valid locations to expand into
steps (int) – the number of times to execute the watershed
border (int) – the distance to remain away from the edge of the image
- Returns
the image with the watershed executed
- Return type
numpy.array


Butters is a weird little creature. She Doesn't like people, yet craves attention. She yowls seemingly for no reason.
You should probably just avoid her.
Butters was born to a life of crime. Doomed to be a stray from day 1. She fought tooth and nail... claw to reach her arch nemesis, Professor Chaos. Chaos, surprised at the sudden confrontation, threw Butters into the waiting hands of an innocent human. Butters mistook this human as a servant of Chaos and proceeded to terrorize them for the rest of her natural life. And probably in death. As a ghost. Cats never forgive.
Check out Frederick here!


Shuffle Functionality Sometimes Not Available
-
ubrgeek
Does "shuffle" need to be turned on in iTunes before it becomes an option in the 'iTunes" portion of the pull-down menu? It seems to be hit-or-miss for when it's an option. (Sorry for the two posts, but trying to see if Synergy does exactly what I need before buying it. Thx.)
-
Greg Hurrell
That menu option should work whenever the corresponding button works in iTunes.
In other words, there may be some playlist or source types for which it doesn't work (for example, in the iTunes Music Store), but it should work in normal playlists. Likewise the hot key for toggling shuffle on and off should work too.
If it doesn't work like you expect, please provide more details so that I can investigate; but my belief is that is works (I think that menu item has been in place for at least a couple of years now, maybe even three, and there haven't been any bugs reported for it).
-
ubrgeek
OK, I'll keep playing with it. Thx. One very last question, if I may - Can Synergy recognize Shared played lists? I've got one that lets me stream music from another box on my network and shows up under the "Shared" playlist in iTunes. However, it doesn't seem to show up under the Playlist menu list.
-
Greg Hurrell
At the moment I can't confirm this as I don't have another machine right now on the local network. I suspect that the shared playlist won't show up in the list but you should still be able to see the track information when playing from it.
Reply
This topic is now closed.