MoMo Results
Modification Motifs
MoMo version 5.0.1 (Release date: Wed Aug 22 15:26:53 2018 -0700)
For further information on how to interpret these results please access http://meme-suite.org/doc/momo-output-format.html .
To get a copy of the MoMo software please access http://meme-suite.org .
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]
Peptide Preprocessing
Algorithm: MoDL
Number of Mods: 435
Number of Mod Types: 3
Number of Mods Passing Filters: 249
Number of Mod Types Passing Filters: 3
Results
motif: xxx_S79.9_xxL score: 26.57 fg: 17/111 bg: 174/2056 fg/bg: 1.8 unadjusted p -value: 1.5e-002
Show/Hide Motif Occurrences
ELKSEGL
KRFSGSL
FSGSLKL
KSHSEGL
NDISKLL
YLESGKL
KHASLIL
HNKSHTL
VLLSRHL
VLRSMEL
DMMSSSL
AQDSPEL
DRYSFSL
FSPSGKL
DCTSLLL
GLLSDSL
DFLSKSL
Show/Hide MoDL Log:
MoDL Log
STEP: 0, DL: 2889.2239
STEP: 1, DL: 2862.6534
xxx_S79.9_xxL
STEP: 2, DL: 2864.4585
xxx_S79.9_xx[LV]
STEP: 3, DL: 2871.9572
xxx_S79.9_xx[HLV]
STEP: 4, DL: 2876.9604
xxx_S79.9_xx[FHLV]
STEP: 5, DL: 2882.2951
xxx_S79.9_xx[FHLRV]
STEP: 6, DL: 2887.2663
xxx_S79.9_xx[FHLRVW]
STEP: 7, DL: 2893.0811
xxx_S79.9_xx[FHLRVWY]
STEP: 8, DL: 2898.1119
xxx_S79.9_xS[FHLRVWY]
STEP: 9, DL: 2890.3195
xxx_S79.9_xS[FHLRVWY]
xxx_S79.9_xxL
STEP: 10, DL: 2862.6534
xxx_S79.9_xxL
STEP: 11, DL: 2864.4585
xxx_S79.9_xx[LV]
STEP: 12, DL: 2871.9572
xxx_S79.9_xx[HLV]
STEP: 13, DL: 2876.9604
xxx_S79.9_xx[FHLV]
STEP: 14, DL: 2882.2951
xxx_S79.9_xx[FHLRV]
STEP: 15, DL: 2887.2663
xxx_S79.9_xx[FHLRVW]
STEP: 16, DL: 2893.0811
xxx_S79.9_xx[FHLRVWY]
STEP: 17, DL: 2898.1119
xxx_S79.9_xS[FHLRVWY]
STEP: 18, DL: 2890.3195
xxx_S79.9_xS[FHLRVWY]
xxx_S79.9_xxL
STEP: 19, DL: 2862.6534
xxx_S79.9_xxL
STEP: 20, DL: 2864.4585
xxx_S79.9_xx[LV]
STEP: 21, DL: 2871.9572
xxx_S79.9_xx[HLV]
STEP: 22, DL: 2876.9604
xxx_S79.9_xx[FHLV]
STEP: 23, DL: 2882.2951
xxx_S79.9_xx[FHLRV]
STEP: 24, DL: 2887.2663
xxx_S79.9_xx[FHLRVW]
STEP: 25, DL: 2893.0811
xxx_S79.9_xx[FHLRVWY]
STEP: 26, DL: 2898.1119
xxx_S79.9_xS[FHLRVWY]
STEP: 27, DL: 2890.3195
xxx_S79.9_xS[FHLRVWY]
xxx_S79.9_xxL
STEP: 28, DL: 2862.6534
xxx_S79.9_xxL
STEP: 29, DL: 2864.4585
xxx_S79.9_xx[LV]
STEP: 30, DL: 2871.9572
xxx_S79.9_xx[HLV]
STEP: 31, DL: 2876.9604
xxx_S79.9_xx[FHLV]
STEP: 32, DL: 2882.2951
xxx_S79.9_xx[FHLRV]
STEP: 33, DL: 2887.2663
xxx_S79.9_xx[FHLRVW]
STEP: 34, DL: 2893.0811
xxx_S79.9_xx[FHLRVWY]
STEP: 35, DL: 2898.1119
xxx_S79.9_xS[FHLRVWY]
STEP: 36, DL: 2890.3195
xxx_S79.9_xS[FHLRVWY]
xxx_S79.9_xxL
STEP: 37, DL: 2862.6534
xxx_S79.9_xxL
STEP: 38, DL: 2864.4585
xxx_S79.9_xx[LV]
STEP: 39, DL: 2871.9572
xxx_S79.9_xx[HLV]
STEP: 40, DL: 2876.9604
xxx_S79.9_xx[FHLV]
STEP: 41, DL: 2882.2951
xxx_S79.9_xx[FHLRV]
STEP: 42, DL: 2887.2663
xxx_S79.9_xx[FHLRVW]
STEP: 43, DL: 2893.0811
xxx_S79.9_xx[FHLRVWY]
STEP: 44, DL: 2898.1119
xxx_S79.9_xS[FHLRVWY]
STEP: 45, DL: 2890.3195
xxx_S79.9_xS[FHLRVWY]
xxx_S79.9_xxL
STEP: 46, DL: 2862.6534
xxx_S79.9_xxL
STEP: 47, DL: 2864.4585
xxx_S79.9_xx[LV]
STEP: 48, DL: 2871.9572
xxx_S79.9_xx[HLV]
STEP: 49, DL: 2876.9604
xxx_S79.9_xx[FHLV]
STEP: 50, DL: 2882.2951
xxx_S79.9_xx[FHLRV]
STEP: 51, DL: 2887.2663
xxx_S79.9_xx[FHLRVW]
Final DL: 2862.6534 ( Decrease: 26.57 )
motif: xxx_T79.9_xx[DP] score: 22.09 fg: 20/90 bg: 176/1629 fg/bg: 2.1 unadjusted p -value: 1.9e-003
Show/Hide Motif Occurrences
VKGTDLP
GMETARD
KDETVAP
RFQTGED
NFETRRP
RAKTTQD
FNLTEND
VDRTFSD
YVKTTTP
GRYTGKP
LRKTHEP
NKETAQD
SRRTVLD
IFKTDLP
PPPTHND
MSETNVD
EFSTKED
SLTTFSP
VPLTEGD
NVKTTHP
Show/Hide MoDL Log:
MoDL Log
STEP: 0, DL: 2333.1920
STEP: 1, DL: 2315.7541
xxx_T79.9_xxD
STEP: 2, DL: 2311.1014
xxx_T79.9_xx[DP]
STEP: 3, DL: 2314.9597
xxx_T79.9_xx[DEP]
STEP: 4, DL: 2319.6498
xxx_T79.9_xx[DEPY]
STEP: 5, DL: 2324.7076
xxx_T79.9_xx[DEHPY]
STEP: 6, DL: 2329.9185
xxx_T79.9_xx[DEHMPY]
STEP: 7, DL: 2335.9159
xxx_T79.9_xx[DEHMPQY]
STEP: 8, DL: 2341.6987
xxx_T79.9_Gx[DEHMPQY]
STEP: 9, DL: 2336.7156
xxx_T79.9_[EG]x[DEHMPQY]
STEP: 10, DL: 2332.0561
xxx_T79.9_[EG]x[DEHMPQRY]
STEP: 11, DL: 2328.2486
xxx_T79.9_[EG]x[DEHMPQRVY]
STEP: 12, DL: 2325.3025
xxx_T79.9_[EG]x[DEHKMPQRVY]
Final DL: 2311.1014 ( Decrease: 22.09 )
motif: xxx_Y79.9_xx[GV] score: 10.61 fg: 16/48 bg: 115/944 fg/bg: 2.7 unadjusted p -value: 1.9e-004
Show/Hide Motif Occurrences
GWKYEDV
AKEYILG
PLLYRSV
DGKYKPG
KEKYEVG
GRFYNDV
AKEYVQG
VNEYVNV
FLSYPVV
GARYYGG
QFFYKNV
LKRYTSV
FLGYKAG
IISYAQG
TFQYTKG
IFIYTDV
Show/Hide MoDL Log:
MoDL Log
STEP: 0, DL: 1224.9882
STEP: 1, DL: 1217.3839
xxx_Y79.9_xxG
STEP: 2, DL: 1214.3815
xxx_Y79.9_xx[GV]
STEP: 3, DL: 1222.2505
xxx_Y79.9_xx[GSV]
STEP: 4, DL: 1225.7014
xxx_Y79.9_xx[GSVW]
STEP: 5, DL: 1230.6287
xxx_Y79.9_xx[FGSVW]
STEP: 6, DL: 1235.5931
xxx_Y79.9_xx[FGNSVW]
STEP: 7, DL: 1240.5674
xxx_Y79.9_xx[FGNPSVW]
STEP: 8, DL: 1240.0635
Gxx_Y79.9_xx[FGNPSVW]
STEP: 9, DL: 1235.4864
[AG]xx_Y79.9_xx[FGNPSVW]
STEP: 10, DL: 1232.2827
[AG]xx_Y79.9_xx[AFGNPSVW]
STEP: 11, DL: 1231.9410
[AG]xx_Y79.9_xx[AFGNPSTVW]
STEP: 12, DL: 1233.9170
[AG]xx_Y79.9_xx[ACFGNPSTVW]
Final DL: 1214.3815 ( Decrease: 10.61 )
DEBUGGING INFORMATION
Command line:
momo modl --oc results/momo18 --psm-type tide --db-background --remove-unknowns T --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: true
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.
Go to top