
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
-
The full set of motif occurences can be seen in the
tab-delimited plain text output file
momo.txt.
-
SUMMARY:
- Number of Mods: 435
- Number of Mod Types: 3
- Number of Mods Passing Filters: 252
- Number of Mod Types Passing Filters: 3
final_pattern: XXX_S79.9_XXL score: 26.8046 foreground_size: 17
- ELKSEGL
- KRFSGSL
- FSGSLKL
- KSHSEGL
- NDISKLL
- YLESGKL
- KHASLIL
- HNKSHTL
- VLLSRHL
- VLRSMEL
- DMMSSSL
- AQDSPEL
- DRYSFSL
- FSPSGKL
- DCTSLLL
- GLLSDSL
- DFLSKSL
MoDL Log
- STEP: 0, DL: 2955.99
- STEP: 1, DL: 2929.18
XXX_S79.9_XXL
- STEP: 2, DL: 2930.76
XXX_S79.9_XX[LV]
- STEP: 3, DL: 2938.11
XXX_S79.9_XX[HLV]
- STEP: 4, DL: 2941.52
XXX_S79.9_XX[HLRV]
- STEP: 5, DL: 2947.11
XXX_S79.9_XX[FHLRV]
- STEP: 6, DL: 2952.28
XXX_S79.9_XX[FHLRVW]
- STEP: 7, DL: 2958.19
XXX_S79.9_XX[FHLRVWY]
- STEP: 8, DL: 2964.09
XXX_S79.9_XX[FHLMRVWY]
- STEP: 9, DL: 2958.34
XSX_S79.9_XX[FHLMRVWY]
- STEP: 10, DL: 2953.26
XSX_S79.9_XX[FHLMRTVWY]
- STEP: 11, DL: 2949.67
XSX_S79.9_XX[FHLMRTVWY]
XXX_S79.9_XXL
- STEP: 12, DL: 2929.18
XXX_S79.9_XXL
- STEP: 13, DL: 2930.76
XXX_S79.9_XX[LV]
- STEP: 14, DL: 2938.11
XXX_S79.9_XX[HLV]
- STEP: 15, DL: 2941.52
XXX_S79.9_XX[HLRV]
- STEP: 16, DL: 2947.11
XXX_S79.9_XX[FHLRV]
- STEP: 17, DL: 2952.28
XXX_S79.9_XX[FHLRVW]
- STEP: 18, DL: 2958.19
XXX_S79.9_XX[FHLRVWY]
- STEP: 19, DL: 2964.09
XXX_S79.9_XX[FHLMRVWY]
- STEP: 20, DL: 2958.34
XSX_S79.9_XX[FHLMRVWY]
- STEP: 21, DL: 2953.26
XSX_S79.9_XX[FHLMRTVWY]
- STEP: 22, DL: 2949.67
XSX_S79.9_XX[FHLMRTVWY]
XXX_S79.9_XXL
- STEP: 23, DL: 2929.18
XXX_S79.9_XXL
- STEP: 24, DL: 2930.76
XXX_S79.9_XX[LV]
- STEP: 25, DL: 2938.11
XXX_S79.9_XX[HLV]
- STEP: 26, DL: 2941.52
XXX_S79.9_XX[HLRV]
- STEP: 27, DL: 2947.11
XXX_S79.9_XX[FHLRV]
- STEP: 28, DL: 2952.28
XXX_S79.9_XX[FHLRVW]
- STEP: 29, DL: 2958.19
XXX_S79.9_XX[FHLRVWY]
- STEP: 30, DL: 2964.09
XXX_S79.9_XX[FHLMRVWY]
- STEP: 31, DL: 2958.34
XSX_S79.9_XX[FHLMRVWY]
- STEP: 32, DL: 2953.26
XSX_S79.9_XX[FHLMRTVWY]
- STEP: 33, DL: 2949.67
XSX_S79.9_XX[FHLMRTVWY]
XXX_S79.9_XXL
- STEP: 34, DL: 2929.18
XXX_S79.9_XXL
- STEP: 35, DL: 2930.76
XXX_S79.9_XX[LV]
- STEP: 36, DL: 2938.11
XXX_S79.9_XX[HLV]
- STEP: 37, DL: 2941.52
XXX_S79.9_XX[HLRV]
- STEP: 38, DL: 2947.11
XXX_S79.9_XX[FHLRV]
- STEP: 39, DL: 2952.28
XXX_S79.9_XX[FHLRVW]
- STEP: 40, DL: 2958.19
XXX_S79.9_XX[FHLRVWY]
- STEP: 41, DL: 2964.09
XXX_S79.9_XX[FHLMRVWY]
- STEP: 42, DL: 2958.34
XSX_S79.9_XX[FHLMRVWY]
- STEP: 43, DL: 2953.26
XSX_S79.9_XX[FHLMRTVWY]
- STEP: 44, DL: 2949.67
XSX_S79.9_XX[FHLMRTVWY]
XXX_S79.9_XXL
- STEP: 45, DL: 2929.18
XXX_S79.9_XXL
- STEP: 46, DL: 2930.76
XXX_S79.9_XX[LV]
- STEP: 47, DL: 2938.11
XXX_S79.9_XX[HLV]
- STEP: 48, DL: 2941.52
XXX_S79.9_XX[HLRV]
- STEP: 49, DL: 2947.11
XXX_S79.9_XX[FHLRV]
- STEP: 50, DL: 2952.28
XXX_S79.9_XX[FHLRVW]
- STEP: 51, DL: 2958.19
XXX_S79.9_XX[FHLRVWY]
Final DL: 2929.18
final_pattern: XXX_T79.9_XX[DP] score: 22.3889 foreground_size: 20
- VKGTDLP
- GMETARD
- KDETVAP
- RFQTGED
- NFETRRP
- RAKTTQD
- FNLTEND
- VDRTFSD
- YVKTTTP
- GRYTGKP
- LRKTHEP
- NKETAQD
- SRRTVLD
- IFKTDLP
- PPPTHND
- MSETNVD
- EFSTKED
- SLTTFSP
- VPLTEGD
- NVKTTHP
MoDL Log
- STEP: 0, DL: 2335.52
- STEP: 1, DL: 2317.92
XXX_T79.9_XXD
- STEP: 2, DL: 2313.13
XXX_T79.9_XX[DP]
- STEP: 3, DL: 2316.85
XXX_T79.9_XX[DEP]
- STEP: 4, DL: 2321.68
XXX_T79.9_XX[DEPY]
- STEP: 5, DL: 2326.69
XXX_T79.9_XX[DEHPY]
- STEP: 6, DL: 2331.87
XXX_T79.9_XX[DEHMPY]
- STEP: 7, DL: 2337.82
XXX_T79.9_XX[DEHMPQY]
- STEP: 8, DL: 2343.92
XXX_T79.9_GX[DEHMPQY]
- STEP: 9, DL: 2338.89
XXX_T79.9_[EG]X[DEHMPQY]
- STEP: 10, DL: 2334.19
XXX_T79.9_[EG]X[DEHMPQRY]
- STEP: 11, DL: 2330.36
XXX_T79.9_[EG]X[DEHMPQRVY]
- STEP: 12, DL: 2327.42
XXX_T79.9_[EG]X[DEHKMPQRVY]
Final DL: 2313.13
final_pattern: XXX_Y79.9_XX[GV] score: 10.8455 foreground_size: 16
- GWKYEDV
- AKEYILG
- PLLYRSV
- DGKYKPG
- KEKYEVG
- GRFYNDV
- AKEYVQG
- VNEYVNV
- FLSYPVV
- GARYYGG
- QFFYKNV
- LKRYTSV
- FLGYKAG
- IISYAQG
- TFQYTKG
- IFIYTDV
MoDL Log
- STEP: 0, DL: 1225.93
- STEP: 1, DL: 1218.21
XXX_Y79.9_XXG
- STEP: 2, DL: 1215.09
XXX_Y79.9_XX[GV]
- STEP: 3, DL: 1223.11
XXX_Y79.9_XX[GSV]
- STEP: 4, DL: 1226.52
XXX_Y79.9_XX[GSVW]
- STEP: 5, DL: 1231.42
XXX_Y79.9_XX[FGSVW]
- STEP: 6, DL: 1236.35
XXX_Y79.9_XX[FGNSVW]
- STEP: 7, DL: 1241.31
XXX_Y79.9_XX[FGNPSVW]
- STEP: 8, DL: 1240.86
GXX_Y79.9_XX[FGNPSVW]
- STEP: 9, DL: 1236.26
[AG]XX_Y79.9_XX[FGNPSVW]
- STEP: 10, DL: 1233.02
[AG]XX_Y79.9_XX[AFGNPSVW]
- STEP: 11, DL: 1232.67
[AG]XX_Y79.9_XX[AFGNPSTVW]
- STEP: 12, DL: 1234.64
[AG]XX_Y79.9_XX[ACFGNPSTVW]
Final DL: 1215.09
DEBUGGING INFORMATION
Command line:
/Users/t.bailey/meme_hg/meme/src/parallel/momo modl --oc results/momo17 --psm-type tide --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt
PARAMETERS:
algorithm: modl
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: false
eliminate repeats: true
eliminate repeat width: 7
min occurrences: 5
single motif per mass: false
hash fasta: false
hash fasta width: 0
max motifs: 100
max iterations: 50
max no decrease iterations: 10
This information can be useful in the event you wish to report a
problem with the MoMo software.
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