| 362 | (A) | and thus are we turnede of owre tyre in takynnynge of the sothe |
| 366 | (C) | Thus ar we turned in tyre . in token of þe soþe |
| 367 | (D) | þus are we turnyd in tyre in tokyn of þe sothe |
| 368 | (E) | loo how we been arayed . in tokne of þe sothe . |
| (Ex) | ---- no text ---- | |
| 376 | (L) | þus ben we tourned of oure tyre in tokne of þe soþe |
| (P) | ---- no text ---- | |
| 360 | (U) | Thus are we turned in tyre / in token of the sothe |
| (V) | ---- no text ---- |


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momo <algorithm> [options] <PTM file>+
The name of the algorithm to use to search for motifs. Available algorithms are simple, motifx, and modl.
The names of one or more files with peptide sequences containing a post-translationally modified amino acid. Each file must be either in PSM format, FASTA format, or "Raw" (one sequence per line) format. All files must use the same format, and MoMo will attempt to determine the format of the file(s) using the following rules, in order:
With FASTA or Raw format files, all sequences must have the same length, the length must be 7 or be specified using the option --width, below, the sequences must be in the Protein IUPAC alphabet, and the modified amino acid is assumed to be the central residue.
With PSM format files, one column must contain the modified peptides with the modified amino acid indicated as described in the PSM format documentation. You can specify the name of the modified peptide column using the --sequence-column, option, below. MoMo will attempt to expand all modified peptides to the width of the longest modified peptide or the requested motif width, whichever is wider. (See option --width, below, for a description of how the expansion is done.)
MoMo writes its output to files in a directory named
momo_out
, which it creates if necessary. You can change the
output directory using the --o or --oc options.
The directory will contain the following files:
momo.html
-
an HTML file that provides the results in an interactive, human-readable formatmomo.txt
-
a plain text file containing the motifs discovered by MoMo in MEME Motif Format<name>.png
-
PNG image files containing sequence logos for each of the
motifs found by MoMo (where <name> is the motif name)
| Option | Parameter | Description | Default Behavior | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| General Options | |||||||||||
| --psm-type | comet| ms-gf+| tide| percolator | If the PTM file(s) are in tab-separated Peptide-Spectrum Match (PSM) format, you can specify the name of the program that created them. This will cause MoMo to set the name of the column containing the modified peptides appropriately. | MoMo will attempt to determine the type of the PTM file(s), and if they are in a PSM format, you must use the --sequence-column option, below. | ||||||||
| --sequence-column | name | The name of the column containing the modified peptides in the PTM file. This option is required if the PTM file(s) are in PSM format unless you use the --psm-type option, above.. | None. | ||||||||
| --width | width | The width of motifs to discover.
Because motifs will be symmetric around the central, modified residue, width
must be odd. The behavior of MoMo depends on the format of the PTM input file(s).
|
FASTA or Raw format: Motifs of width 7 are generated. PSM format: Motifs of width the length of the longest modified peptide are generated. |
||||||||
| --protein-database | protein database file | A protein database that will be used to allow expansion of modified peptides
from PSM formatted PTM input file(s)
(see option --width, above),
and for estimating the amino acid background frequencies.
(This is typically the protein database that was used to generate the PTM input file(s).)
This file may be in either FASTA or Raw format.
If it is in FASTA format, the sequences may be of any length.
If it is in Raw format, each sequence must be of the length specified by the
--width option, above, and there must be exactly one sequence per line,
with no sequence ID lines.
The background frequencies are used as follows:
|
Modified peptides from PTM file(s) in PSM format are padded using the Protein IUPAC 'X' character as required, and the amino acid background frequencies are derived from the frequencies in the NCBI non-redundant protein database as of September 22, 1996. | ||||||||
| --filter | field,lt|le|eq|ge|gt,threshold | Specifies a (single) filter that causes only modified peptides that pass the given test to be included in the analysis. The test consists of three components separated by commas with no spaces in between. (If the field name contains spaces, enclose the entire test string in quotes.) The field component of the parameter specifies the name of the column in the PSM format PTM file from which the score is drawn. The next component specifies whether only modified peptides with scores less than (lt), less than or equal (le), equal (eq), greater than or equal (ge), or greater than (gt) the threshold are retained. | No filter. | ||||||||
| --remove-unknowns | T|F | If TRUE (T), all modified peptides that contain an 'X' (after expansion and padding, see option --width, above) will be removed from the analysis. | Do not remove sequences just because they contain an 'X'. | Remove sequences if they contain an 'X'. | |||||||
| --eliminate-repeats | num | Any groups of modified peptides whose num central residues (after expansion and padding, see option --width, above) are identical will be replaced with a single copy. Because the window is symmetric around the central, modified residue, num must be odd. To turn this option off, specify a width of 0. Note: Since shorter peptides will be padded with the 'X' character, which matches any other character, shorter peptides will match longer ones that contain them, and will be subject to elimination. | Behave as if the value width (see option --width, above) was given for num. | ||||||||
| --min-occurrences | num | Only attempt to construct a motif for a particular modification of an amino acid if there are at least num modified peptides (after eliminating repeats, see option --eliminate-repeats, above) that contain it. Furthermore, only motifs containing at least num modified peptides will be reported. | Behave as if 0 was given for num. | ||||||||
| --min-occurrences | num | The minimum number of sequences in the post-translationally modified data set needed to match the residue/position pair for each recursive iteration of motif-x. MoMo only attempts to construct a motif for a particular modification of an amino acid if there are at least num modified peptides (after eliminating repeats, see option --eliminate-repeats, above) that contain it. | Behave as if 20 was given for num. | ||||||||
| --single-motif-per-mass | Generate a single motif that combines all central residues that have the same modification mass. Only valid with PSM formatted PTM files. (The modification mass is given as a number following the modified amino acid in the modified peptide as described in the PSM format documentation.) For example, phosphorylation is typically specified as a mass of 79.97 added to the residues S, T or Y. If this option is not given, three separate motifs are generated, each with a perfectly conserved central residue. If this option is given, then all the phosphorylation events are combined into a single motif, with a mixture of S, T and Y in the central position. | Generate a motif for each combination of residue and modification mass. | |||||||||
| --hash-fasta | k | If a protein database is provided in FASTA format, the process of finding the location of a peptide within the protein can be sped up using an O(1) lookup table hashing from each unique k-mer to an arraylist of locations. If k is 0, the program will proceed using linear search instead of creating a lookup table. Note: With a full mammalian proteome as the protein database, MoMo will typically run faster using hashing (e.g., set k to 6) if your PTM file(s) contain more than 50,000 peptide sequences in total. | Behave as if 0 was given for k. | ||||||||
| --max-motifs | num | MoDL will stop after it finds num motifs. | Behave as if 100 was given for num. | ||||||||
| --max-iterations | num | MoDL will stop after num iterations. | Behave as if 50 was given for num. | ||||||||
| --max-no-decrease | num | MoDL will stop if there is no decrease in MDL for num iterations. | Behave as if 10 was given for num. | ||||||||
| --score-threshold | num | The largest binomial probability for a residue/position pair to be counted as significant during each recursive iteration of motif-x. | Behave as if 1e-6 was given for num. | ||||||||
| --harvard | Mimic the behavior of (the Harvard version of) motif-x more closely by only calculating binomial p-values no smaller than 10-16 for residue/position pairs. Smaller p-values are set to 10-16, and ties are broken by sorting residue/position pairs by decreasing number of peptides that match them. | Calculate residue/position pair binomial p-values in log-space, allowing p-values as small as e(-10300). | |||||||||
If you use MoMo in your research, please cite the following paper: A. Cheng, C. E. Grant, T. L. Bailey and W. S. Noble, "MoMo: Discovery of post-translational modification motifs", bioRxiv, preprint, 2017. [full text]


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‘If I weren’t singing, I would be a masseur’
by Doreen NanziriKenneth Mugabi is a unique and memorable singer, songwriter and guitarist. He first claimed the limelight as one of the contestants of Coca-Cola Rated Next talent show, then became a regular performer at the Milege Acoustic Jazz Project every Thursday at Makerere University guesthouse where patrons adore his voice and storytelling skill. Quick Talk talked to the Kibunomu singer shortly before his recent show at the National Theatre where the interview was constantly interrupted by phone calls…
Good evening, Kenneth!
Yes, good evening!
How would you describe Kenneth Mugabi?
Kenneth Mugabi is an artist, soulful performer, artiste and greatly known for my Naki song.
I went to Kibiri Church of Uganda primary school then, Lubiri High School [O-level], Makerere High School for my A-level and Makerere University where I pursued a BA in Film and Drama.
Who inspired you to join the singing competition?
You know when there is something inside you that wants to come out? Like a caged bird. So, for me it was more of something that I wanted to release. The talent was in me because my mother used to sing and write church songs at St Luke’s Church of Uganda, Kibuye.
Talking about caged birds, is that why you failed with school choirs?
[Laughs, slapping a hand to his forehead] Well, at Kibuye primary school, I was recruited in the choir three times but each time I would run away. I did not want to be part of them because kiboko zali nyingi ennaku ezo, yaye mama nze! [there was a lot of caning back then]. I, however, enjoyed being part of them and had to find ways of not being part of them, yet always be around. [He and his friends followed the rehearsals from the windows].
How could that benefit you?
Actually I learnt playing most instruments just by watching from the window.
Why Afro soul music?
[After a long silence] I would say that soul recognises soul. It’s like a Muganda going to Gulu and suddenly meets a fellow Muganda; you will start speaking and feel like you are home. That is me with soul music. I used to listen to Paul Kafeero, Fred Ssebata, [and] Lucky Dube because my mother used to listen to that. Kadongokamu inspired me a lot [One can recognise that influence in Mugabi’s storytelling and guitar skills].
Along the way, Mowzey Radio came and I was touched; he was so different. Morris Kirya also had something different. I went picking something from all these musicians and came up with my own genre, Afro soul.
I see; by the way Kenneth, what would you be doing if not singing?
I think acting.
Have you ever tried it before?
Yeah. I even act in my songs [chuckles]
And outside the arts?
Aahh… maybe [be a masseur], travelling, if it was paying [It does, if you are a cabin crew member on some airline…] I am also fascinated by farming and dealing in local medicine. I rarely go to hospital; [my theory is:] if you are suffering from anything, take a glass of aloe vera.
But why masseur coming at the top?
I was thinking out loud [laughs]… massage is more like medicine; so, it is not surprising, because even my music massages the soul so, there is a connection.
Away from that, what is your most memorable moment?
Strings Of My Soul, which was my first concert. It was so exhausting but very interesting. How I wish it lasted longer, but it was just hours. It was my first concert but people enjoyed and I too enjoyed seeing people enjoy.
Did life change thereafter?
Yes, of course! People’s enjoyment elevated me, after struggling all those years. This particular concert made everything easy because I am releasing an album this year.
Do you have a ‘most embarrassing moment’?
 [He whistles and shakes his head in wonder] I remember it was Embuutu y’Embutikizi [an annual music gala by Bukedde FM]. I walked up to Makindye from Nakivubo to release the anger. By the way it was so recent, after Coca-Cola Rated Next.
Such embarrassments can turn out to be a motivation.
Well, I am sure that some of those who chased me off that stage are enjoying Naki.
Sorry about that, man. What do you do in your free time?
If I am not writing songs and doing my business, I am always home helping out my sisters with house chores [aww! The image of that…], then I go out the do corporate social responsibility.
Ok…when do you spend time with your ‘Naki’? Could you be single?
Do you have an application – pending or otherwise?
Hahaha! No. Really!
Why! Do I look ugly?
Hahaha, don’t change the subject; are you single, searching or married?
I am not married, that’s all I can say, because you can be seeing someone but you don’t know what will happen ... I prefer saying I’m not married yet, instead of saying that I’m seeing someone, because I might say it today and she goes the next day.
Such pessimism! OK, who is your ideal woman?
Physically, a woman who is not that into makeup.  All the rest can be handled but she has to be smart because I don’t want someone who is very dependent. I know we are supposed to take care of you, but she isn’t supposed to over depend on me until we are married because once married, then you are my responsibility. I would also like someone who sees things quickly and does not fear me.
[Exhales heavily] I hope I won’t end up alone, because of what I want.
Hmmm, you might be one of those stingy men I hear about!
Me!? My name is Mugabi [it means giver in Luganda]; so, I can’t be stingy at all. By the way, there are things that don’t make sense, which girls do, like being jealous yet you’re not allowed to be.
Shaaa! Jealousy is part of love!
Here is the thing, I have gone for introduction at your home; so, why be jealous?
To take you back though, I think every woman needs a little makeup sometimes...
Makingup is fine but, she has to be comfortable without makeup, because there are those not comfortable without it. I want a woman who comfortably lives without it.
How do you express the romantic side of you?
A mere listening to my music will give you a real picture of it all.
Wapi! Sometimes you people sing the reverse of what is happening in your real lives.
Life is not a movie; for example, me before dating a girl, I first give you a hard time for quite some time and see if you can persist. By the way, I give people a hard time but all this is to help me know who you truly are, your dos and don’ts and see if I can persist too.
I receive calls but I don’t call; I call when I want to call but not when I have to call or when you want me to call; I do things my way than doing them other people’s ways. [Eh! Yes, Quick Talk hopes you don’t end up alone, brother.]
Now, if you were president for a day…
I would focus on job creation than job seeking and change the education system. Ugandans are creative but they don’t know where to start from; so, I would really provide such platforms for the youth.
nanziridoreen88@gmail.com


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