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: 252
Number of Mod Types Passing Filters: 3
Results
motif: xxx_S79.9_[CIR]xx score: 12.60 fg: 16/114 bg: 4/114 fg/bg: 4.0 unadjusted p -value: 4.3e-003
Show/Hide Motif Occurrences
GALSRTH
SSTSRYM
PAKSIEG
GIHSRRK
KRMSCII
EYISRYE
KIQSCQD
VLLSRHL
IYSSRGV
AQTSIDT
SSHSIKY
LNFSRPW
EPVSISF
PTESRKN
EEQSIND
LSSSIGV
motif: xxx_S79.9_xx[GN] score: 8.99 fg: 15/114 bg: 5/114 fg/bg: 3.0 unadjusted p -value: 1.6e-002
Show/Hide Motif Occurrences
DTASKFG
PRDSDDN
ELQSLLG
MIYSSRG
SVSSNSN
VVESPEG
PISSKYN
XXMSESN
HEHSKAN
XXMSETN
ALTSFLG
TTFSPSG
DAESALN
Show/Hide MoDL Log:
MoDL Log
STEP: 0, DL: 3025.5385
STEP: 1, DL: 2996.3377
xxx_S79.9_Rxx
STEP: 2, DL: 2981.1369
xxx_S79.9_Rxx
xxx_S79.9_xxN
STEP: 3, DL: 2977.8021
xxx_S79.9_xxN
xxx_S79.9_[CR]xx
STEP: 4, DL: 2978.0091
xxx_S79.9_[CR]xx
xxx_S79.9_xx[GN]
STEP: 5, DL: 2976.9484
xxx_S79.9_xx[GN]
xxx_S79.9_[CIR]xx
STEP: 6, DL: 2977.0430
xxx_S79.9_xx[GN]
xxx_S79.9_[CIPR]xx
STEP: 7, DL: 2978.8971
xxx_S79.9_xx[GN]
xxx_S79.9_[CIMPR]xx
STEP: 8, DL: 2982.0647
xxx_S79.9_[CIMPR]xx
xxx_S79.9_xx[GNY]
STEP: 9, DL: 2981.9136
xxx_S79.9_[CIMPR]xx
xxx_S79.9_xx[DGNY]
STEP: 10, DL: 2982.4116
xxx_S79.9_[CIMPR]xx
xxx_S79.9_xx[DGNWY]
STEP: 11, DL: 2983.4851
xxx_S79.9_[CHIMPR]xx
STEP: 12, DL: 2986.4049
xxx_S79.9_[ACHIMPR]xx
STEP: 13, DL: 2990.9867
xxx_S79.9_[ACDHIMPR]xx
STEP: 14, DL: 2996.8083
xxx_S79.9_[ACDHIMPQR]xx
STEP: 15, DL: 3003.4964
xxx_S79.9_[ACDHIMPQRW]xx
Final DL: 2976.9484 ( Decrease: 48.59 )
motif: [FLV]xx_T79.9_xxx score: 43.93 fg: 26/90 bg: 7/90 fg/bg: 3.7 unadjusted p -value: 2.0e-004
Show/Hide Motif Occurrences
VKGTDLP
VRGTPVE
FSSTSRY
LKVTCLS
FDDTNPE
FWVTNLK
LIETQRS
LMKTVWA
FNLTEND
VDRTFSD
VKTTTPA
VKDTIDF
LRKTHEP
VNNTRTH
LAFTLGV
VDDTRTT
LWDTNYA
VALTSFL
VPLTEGD
VKTTHPV
FSLTTFS
FQYTKGR
FIYTDVL
VDCTLAT
LDCTSLL
VKPTLSF
Show/Hide MoDL Log:
MoDL Log
STEP: 0, DL: 2428.4381
STEP: 1, DL: 2398.6503
Vxx_T79.9_xxx
STEP: 2, DL: 2384.5884
[FV]xx_T79.9_xxx
STEP: 3, DL: 2384.5046
[FLV]xx_T79.9_xxx
STEP: 4, DL: 2384.9833
[FGLV]xx_T79.9_xxx
STEP: 5, DL: 2387.8685
[FGLMV]xx_T79.9_xxx
STEP: 6, DL: 2390.6240
[FGLMVY]xx_T79.9_xxx
STEP: 7, DL: 2395.1328
[FGLMTVY]xx_T79.9_xxx
STEP: 8, DL: 2400.0159
[FGLMTVWY]xx_T79.9_xxx
STEP: 9, DL: 2405.3408
[FGLMQTVWY]xx_T79.9_xxx
STEP: 10, DL: 2411.2529
[FGILMQTVWY]xx_T79.9_xxx
STEP: 11, DL: 2416.8906
[CFGILMQTVWY]xx_T79.9_xxx
STEP: 12, DL: 2422.0374
[CFGHILMQTVWY]xx_T79.9_xxx
STEP: 13, DL: 2429.8155
[CDFGHILMQTVWY]xx_T79.9_xxx
Final DL: 2384.5046 ( Decrease: 43.93 )
motif: xx[EK]_Y79.9_xxx score: 13.64 fg: 15/48 bg: 5/48 fg/bg: 3.0 unadjusted p -value: 1.1e-002
Show/Hide Motif Occurrences
IAKYEAL
HMKYNDN
GWKYEDV
VREYLES
AKEYILG
LQEYLDK
YAKYLIE
TIKYVLE
AFEYARA
DGKYKPG
KEKYEVG
AKEYVQG
VNEYVNV
ATKYLVN
SNKYAVA
Show/Hide MoDL Log:
MoDL Log
STEP: 0, DL: 1337.9541
STEP: 1, DL: 1327.6881
xxE_Y79.9_xxx
STEP: 2, DL: 1324.3170
xx[EK]_Y79.9_xxx
STEP: 3, DL: 1329.5658
xx[EKR]_Y79.9_xxx
STEP: 4, DL: 1331.3450
xx[CEKR]_Y79.9_xxx
STEP: 5, DL: 1331.8127
xx[CEKNR]_Y79.9_xxx
STEP: 6, DL: 1331.5108
xx[CEKNRW]_Y79.9_xxx
STEP: 7, DL: 1335.1113
xx[CDEKNRW]_Y79.9_xxx
STEP: 8, DL: 1338.3831
xx[CDEKNPRW]_Y79.9_xxx
STEP: 9, DL: 1342.3920
xx[CDEKNPRTW]_Y79.9_xxx
STEP: 10, DL: 1346.4961
xx[CDEHKNPRTW]_Y79.9_xxx
STEP: 11, DL: 1350.2086
xx[CDEHKMNPRTW]_Y79.9_xxx
STEP: 12, DL: 1351.4662
xx[CDEHKMNPRTW]_Y79.9_xIx
Final DL: 1324.3170 ( Decrease: 13.64 )
DEBUGGING INFORMATION
Command line:
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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