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:
Algorithm: motif-x
Number of Mods: 252
Number of Mod Types: 3
Number of Mods Passing Filters: 249
Number of Mod Types Passing Filters: 3
final_pattern: XXX_S_GXL score: 3.82 foreground_matches: 3 foreground_size: 111 bg_matches: 5 bg_size: 2057 fold_increase: 11.12 E-value: 1.8e+000
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final_pattern: XXX_S_XGX score: 1.49 foreground_matches: 13 foreground_size: 108 bg_matches: 140 bg_size: 2052 fold_increase: 1.76 E-value: 8.4e+000
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EGKSLGI
RMHSAGK
ELKSEGL
KSHSEGL
NSASSGP
PNPSTGK
IYSSRGV
NGVSYGR
CPNSTGA
IRISEGI
RLVSNGT
HPVSHGH
LSSSIGV
final_pattern: XXL_T_EXX score: 3.50 foreground_matches: 4 foreground_size: 90 bg_matches: 10 bg_size: 1629 fold_increase: 7.24 E-value: 1.4e+000
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KQLTEGV
KDLTEFL
FNLTEND
VPLTEGD
final_pattern: XRY_T_XXX score: 2.91 foreground_matches: 2 foreground_size: 86 bg_matches: 3 bg_size: 1619 fold_increase: 12.55 E-value: 6.8e+000
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final_pattern: XXX_T_XXD score: 1.33 foreground_matches: 9 foreground_size: 84 bg_matches: 91 bg_size: 1616 fold_increase: 1.90 E-value: 1.2e+001
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GMETARD
RFQTGED
RAKTTQD
VDRTFSD
NKETAQD
SRRTVLD
PPPTHND
MSETNVD
EFSTKED
final_pattern: RXX_T_XPX score: 2.89 foreground_matches: 2 foreground_size: 75 bg_matches: 3 bg_size: 1525 fold_increase: 13.56 E-value: 5.9e+000
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final_pattern: XXE_T_XXP score: 3.19 foreground_matches: 2 foreground_size: 73 bg_matches: 2 bg_size: 1522 fold_increase: 20.85 E-value: 3.5e+000
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final_pattern: XXX_T_GXE score: 3.04 foreground_matches: 3 foreground_size: 71 bg_matches: 7 bg_size: 1520 fold_increase: 9.18 E-value: 2.4e+000
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final_pattern: VKX_T_XXX score: 3.73 foreground_matches: 5 foreground_size: 68 bg_matches: 15 bg_size: 1513 fold_increase: 7.42 E-value: 3.6e-001
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VKGTDLP
VKTTTPA
VKDTIDF
VKTTHPV
VKPTLSF
final_pattern: XXV_T_XXK score: 3.38 foreground_matches: 3 foreground_size: 63 bg_matches: 6 bg_size: 1498 fold_increase: 11.89 E-value: 1.3e+000
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final_pattern: XEL_T_XXX score: 2.87 foreground_matches: 3 foreground_size: 60 bg_matches: 9 bg_size: 1492 fold_increase: 8.29 E-value: 2.8e+000
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final_pattern: XXC_T_XXX score: 1.33 foreground_matches: 3 foreground_size: 57 bg_matches: 21 bg_size: 1483 fold_increase: 3.72 E-value: 1.2e+001
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final_pattern: AKE_Y_XXG score: 3.67 foreground_matches: 2 foreground_size: 48 bg_matches: 2 bg_size: 944 fold_increase: 19.67 E-value: 5.2e+000
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final_pattern: XXX_Y_XDV score: 3.54 foreground_matches: 3 foreground_size: 46 bg_matches: 6 bg_size: 942 fold_increase: 10.24 E-value: 2.0e+000
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final_pattern: XXR_Y_TXX score: 2.90 foreground_matches: 2 foreground_size: 43 bg_matches: 3 bg_size: 936 fold_increase: 14.51 E-value: 5.2e+000
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final_pattern: XXX_Y_XXG score: 1.56 foreground_matches: 6 foreground_size: 41 bg_matches: 53 bg_size: 933 fold_increase: 2.58 E-value: 7.2e+000
Show/Hide Motif Occurrences
DGKYKPG
KEKYEVG
GARYYGG
FLGYKAG
IISYAQG
TFQYTKG
final_pattern: XXI_Y_RXX score: 3.01 foreground_matches: 2 foreground_size: 35 bg_matches: 3 bg_size: 880 fold_increase: 16.76 E-value: 4.0e+000
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final_pattern: XXX_Y_VXX score: 1.42 foreground_matches: 5 foreground_size: 33 bg_matches: 50 bg_size: 877 fold_increase: 2.66 E-value: 9.5e+000
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AKAYVQF
TIKYVLE
VNEYVNV
VEGYVGR
SFVYVVS
final_pattern: XXR_Y_XFX score: 2.99 foreground_matches: 2 foreground_size: 28 bg_matches: 3 bg_size: 827 fold_increase: 19.69 E-value: 2.9e+000
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DEBUGGING INFORMATION
Command line:
/Users/t.bailey/meme_hg/meme/src/parallel/momo motifx --oc results/momo13 --protein-database momo/small-yeast.fasta --score-threshold 0.05 --min-occurrences 1 momo/small-tide-mod-phospho.txt
PARAMETERS:
algorithm: motif-x
post-translationally modified peptide filenames:
file 1: momo/small-tide-mod-phospho.txt
PTM filetype: Raw
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: 1
single motif per mass: false
hash fasta: false
hash fasta width: 0
score threshold: 0.05
p-value calculations: accurate
This information can be useful in the event you wish to report a
problem with the MoMo software.
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