MoMo version 5.0.2 (Release date: Thu Aug 30 14:26:08 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]

High-scoring Motif Occurences Debugging Information Results in TSV format Results in MEME format


Peptide Preprocessing

Results
  • motif: xxxxxx_S79.9_PxxxxT score: 64.06 fg: 26/1062 bg: 2/1062 fg/bg: 13.0 unadjusted p-value: 1.3e-006 tests: 243 adjusted p-value: 3.2e-004
    sequence logo of motif


  • motif: xxxxxx_S79.9_Pxxxxx score: 44.37 fg: 291/1062 bg: 110/1062 fg/bg: 2.6 unadjusted p-value: 2.1e-024 tests: 231 adjusted p-value: 4.8e-022
    sequence logo of motif


  • motif: xxxRxx_S79.9_xxxxxx score: 11.83 fg: 134/1062 bg: 60/1062 fg/bg: 2.2 unadjusted p-value: 1.4e-008 tests: 166 adjusted p-value: 2.3e-006
    sequence logo of motif


  • motif: xxxxxx_S79.9_Dxxxxx score: 10.62 fg: 85/1062 bg: 50/1062 fg/bg: 1.7 unadjusted p-value: 1.2e-003 tests: 158 adjusted p-value: 1.7e-001
    sequence logo of motif


  • motif: xxxxxx_T79.9_Pxxxxx score: 9.77 fg: 69/296 bg: 31/296 fg/bg: 2.2 unadjusted p-value: 2.1e-005 tests: 83 adjusted p-value: 1.7e-003
    sequence logo of motif


    • DEBUGGING INFORMATION

    Command line: 

    momo motifx -oc /media/bayegy/disk1/bioin3/phop/output/test/outdir/Result/2.Modification_motifs/ --verbosity 1 --sequence-column 'Modified sequence' --width 13 --protein-database /media/bayegy/disk1/bioin3/phop/input/test/abundance/all_sample.fa --eliminate-repeats 13 --min-occurrences 20 --score-threshold 1.0E-6 /media/bayegy/disk1/bioin3/phop/input/test/abundance/peptide_label.txt

    PARAMETERS:

algorithm: motif-x
post-translationally modified peptide filenames: 
	file 1: /media/bayegy/disk1/bioin3/phop/input/test/abundance/peptide_label.txt
PTM filetype: PSM
modified peptide column: 'Modified sequence'
protein database filename: /media/bayegy/disk1/bioin3/phop/input/test/abundance/all_sample.fa
protein database format: FASTA
motif width: 13
filter: false
remove unknowns: true
eliminate repeats: true
	eliminate repeat width: 13
min occurrences: 20
single motif per mass: false
hash fasta: false
	hash fasta width: 0
score threshold: 1e-06
binomial 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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