
MoMo Results
Modification Motifs
MoMo version 5.0.0 (Release date: Fri Sep 29 13:40:17 2017 -0700)
For further information on how to interpret these results
or to get a copy of the MoMo software please access
http://meme.nbcr.net
If you use MoMo in your research, please cite the following paper:
Alice Cheng, Charles Grant, Timothy L. Bailey and William Noble, "MoMo: Discovery of post-translational modification motifs", bioRxiv, preprint, 2017.
[full text]
Results
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The full set of motif occurences can be seen in the
tab-delimited plain text output file
momo.txt.
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SUMMARY:
- Number of Mods: 435
- Number of Mod Types: 1
- Number of Mods Passing Filters: 249
- Number of Mod Types Passing Filters: 1
final_pattern: XRX_79.9_XXX score: 2.20312 foreground_matches: 21 foreground_size: 249 bg_matches: 214 bg_size: 4630
- MRITVNG
- VRGTPVE
- KRFSGSL
- VRGSSQQ
- KRMSCII
- PRNSTIP
- ERVTEPV
- VREYLES
- RRPTNPF
- PRDSDDN
- LRKSPFY
- GRFYNDV
- IRDSVTY
- GRYTGKP
- LRKTHEP
- SRRTVLD
- IRISEGI
- KRYTSVS
- GRFYSLW
- DRYSFSL
- SRWYTLL
DEBUGGING INFORMATION
Command line:
/Users/t.bailey/meme_hg/meme/src/parallel/momo motifx --oc results/momo12 --psm-type tide --protein-database momo/small-yeast.fasta --score-threshold 0.05 --count-threshold 1 --single-motif-per-mass T momo/small-tide-mod.txt
PARAMETERS:
algorithm: motifx
post-translationally modified peptide filenames:
file 1: momo/small-tide-mod.txt
PTM filetype: tide
modified peptide column: 'sequence'
protein database filename: momo/small-yeast.fasta
protein database format: FASTA
motif width: 7
filter: false
remove unknowns: true
eliminate repeats: true
eliminate repeat width: 7
min occurrences: 0
single motif per mass: true
hash fasta: false
hash fasta width: 0
count threshold: 1
score threshold: 0.05
This information can be useful in the event you wish to report a
problem with the MoMo software.
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