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: simple
Number of Mods: 435
Number of Mod Types: 3
Number of Mods Passing Filters: 218
Number of Mod Types Passing Filters: 3
final_pattern: S79.9 foreground_matches: 104
Show/Hide Motif Occurrences
EGKSLGI
KKQSGLA
GALSRTH
RMHSAGK
ELKSEGL
SSTSRYM
KRFSGSL
RGSSQQP
VRGSSQQ
FSGSLKL
PAKSIEG
GIHSRRK
XMMSVNR
KRMSCII
DNSSATK
PRNSTIP
KKLSSAE
KSHSEGL
GLKSHSE
KTRSYNW
IKGSDLV
EYISRYE
NSRSGDT
TCLSNKE
DTASKFG
NDISKLL
YLESGKL
KHASLIL
EGTSFRR
RPGSKFH
PRDSDDN
CWRSDTP
TKGSMHD
KEISDVF
ELQSLLG
SMGSGKS
LRKSPFY
WANSSRF
SDNSASS
NSASSGP
KIQSCQD
SASSGPK
PNPSTGK
IYSSRGV
VKNSPWV
MIYSSRG
NGVSYGR
VLRSMEL
VNNSFYK
RVISVSS
AQTSIDT
SVSSNSN
IRDSVTY
SSNSNSR
SEQSKVK
AATSEQS
DMMSSSL
AQDSPEL
GEVSVFV
HFLSYPV
DFGSAVV
VVESPEG
ETLSKVS
IRISEGI
PISSKYN
MMSSSLR
VPISSKY
MSSSLRH
VIVSGIV
HSSSHSI
KTASEFD
SSHSIKY
EFDSAIA
TAHSSSH
XXMSESN
HEHSKAN
DDRSKPV
KIISYAQ
HLESVVR
LNISGEF
DEFSTKE
LNFSRPW
DRYSFSL
PGDSLYC
YSFSLTT
FSPSGKL
TTFSPSG
RLVSNGT
GTDSHMV
AEWSGLS
HPVSHGH
VSISFLK
EPVSISF
PTESRKN
ELLSHIA
DCTSLLL
GLLSDSL
DAESALN
RKISAVS
SAVSTYF
PTLSFKQ
GVVSKDT
EEQSIND
LSSSIGV
final_pattern: T79.9 foreground_matches: 75
Show/Hide Motif Occurrences
VKGTDLP
DKKTGAE
MRITVNG
VRGTPVE
RVITGNK
YGVTDKI
FSSTSRY
KQLTEGV
GMETARD
RNSTIPT
KEQTEAA
ERVTEPV
KDETVAP
EPVTKAL
TDATFIR
ANRTDAT
SLDTFIK
WIDTASK
GELTRSS
LKVTCLS
RFQTGED
RIFTEEM
RRPTNPF
NFETRRP
AAATAAM
FDDTNPE
FWVTNLK
SLKTYFF
LIETQRS
RAKTTQD
MELTANE
LMKTVWA
PAMTTRG
VDRTFSD
NPSTGKY
KKCTING
AGVTPTK
EELTGVR
RGITIDI
VKTTTPA
PAATSEQ
KTTTPAA
SIDTLKL
GRYTGKP
VKDTIDF
LRKTHEP
KKVTAVV
SRRTVLD
IFKTDLP
VNNTRTH
LAFTLGV
PPPTHND
VDDTRTT
QFKTASE
KRYTSVS
MSETNVD
VALTSFL
EFSTKED
SLTTFSP
YGTTETQ
VKTTHPV
FSLTTFS
NIPTESR
ELFTSLG
FQYTKGR
PDETTFQ
FIYTDVL
EFPTGKE
TLATVDH
VDCTLAT
LDCTSLL
NEWTLDS
AVSTYFE
VKPTLSF
RWYTLLE
final_pattern: Y79.9 foreground_matches: 39
Show/Hide Motif Occurrences
EKSYEIL
IAKYEAL
HMKYNDN
VREYLES
AKAYVQF
AKEYILG
PLLYRSV
LKTYFFS
QGIYRYL
YAKYLIE
VIRYAFE
TIKYVLE
AFEYARA
DGKYKPG
KSRYWYF
NSFYKFL
GRFYNDV
GVSYGRA
AKEYVQG
VEGYVGR
IGRYTGK
FLSYPVV
GARYYGG
ALCYSIS
DTNYAKI
FLGYKAG
IISYAQG
GRFYSLW
TDRYSFS
SNKYAVA
TGPYGKA
IGLYKVI
GLDYHHP
TFQYTKG
IFIYTDV
SFVYVVS
VLLYNAK
MEQYRWD
SRWYTLL
DEBUGGING INFORMATION
Command line:
/Users/t.bailey/meme_hg/meme/src/parallel/momo simple --oc results/momo5 --psm-type tide --eliminate-repeats 3 --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt
PARAMETERS:
algorithm: simple
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: 3
min occurrences: 5
single motif per mass: false
hash fasta: false
hash fasta width: 0
This information can be useful in the event you wish to report a
problem with the MoMo software.
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