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]

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



Peptide Preprocessing



Results

  • motif: xxx_S_GxL score: 3.84 fg: 3/111 bg: 5/2056 fg/bg: 11.1 unadjusted p-value: 6.1e-003
    sequence logo of motif


  • motif: xxx_S_xGx score: 1.48 fg: 13/111 bg: 140/2056 fg/bg: 1.7 unadjusted p-value: 4.5e-002
    sequence logo of motif


  • motif: xxL_T_Exx score: 3.50 fg: 4/90 bg: 10/1629 fg/bg: 7.2 unadjusted p-value: 4.7e-003
    sequence logo of motif


  • motif: xRY_T_xxx score: 2.91 fg: 2/90 bg: 3/1629 fg/bg: 12.1 unadjusted p-value: 2.4e-002
    sequence logo of motif


  • motif: xxx_T_xxD score: 1.33 fg: 11/90 bg: 93/1629 fg/bg: 2.1 unadjusted p-value: 1.7e-002
    sequence logo of motif


  • motif: Rxx_T_xPx score: 2.89 fg: 2/90 bg: 3/1629 fg/bg: 12.1 unadjusted p-value: 2.4e-002
    sequence logo of motif


  • motif: xxE_T_xxP score: 3.19 fg: 2/90 bg: 2/1629 fg/bg: 18.1 unadjusted p-value: 1.5e-002
    sequence logo of motif


  • motif: xxx_T_GxE score: 3.04 fg: 3/90 bg: 7/1629 fg/bg: 7.8 unadjusted p-value: 1.3e-002
    sequence logo of motif


  • motif: VKx_T_xxx score: 3.73 fg: 5/90 bg: 16/1629 fg/bg: 5.7 unadjusted p-value: 3.7e-003
    sequence logo of motif


  • motif: xxV_T_xxK score: 3.38 fg: 3/90 bg: 6/1629 fg/bg: 9.1 unadjusted p-value: 9.3e-003
    sequence logo of motif


  • motif: xEL_T_xxx score: 2.87 fg: 3/90 bg: 9/1629 fg/bg: 6.0 unadjusted p-value: 2.2e-002
    sequence logo of motif


  • motif: xxC_T_xxx score: 1.33 fg: 3/90 bg: 22/1629 fg/bg: 2.5 unadjusted p-value: 1.4e-001
    sequence logo of motif


  • motif: AKE_Y_xxG score: 3.67 fg: 2/48 bg: 2/944 fg/bg: 19.7 unadjusted p-value: 1.3e-002
    sequence logo of motif


  • motif: xxx_Y_xDV score: 3.54 fg: 3/48 bg: 6/944 fg/bg: 9.8 unadjusted p-value: 7.3e-003
    sequence logo of motif


  • motif: xxR_Y_Txx score: 2.90 fg: 2/48 bg: 3/944 fg/bg: 13.1 unadjusted p-value: 2.1e-002
    sequence logo of motif


  • motif: xxx_Y_xxG score: 1.56 fg: 8/48 bg: 56/944 fg/bg: 2.8 unadjusted p-value: 9.2e-003
    sequence logo of motif


  • motif: xxI_Y_Rxx score: 3.01 fg: 2/48 bg: 5/944 fg/bg: 7.9 unadjusted p-value: 4.1e-002
    sequence logo of motif


  • motif: xxx_Y_Vxx score: 1.42 fg: 6/48 bg: 56/944 fg/bg: 2.1 unadjusted p-value: 7.2e-002
    sequence logo of motif


  • motif: xxR_Y_xFx score: 2.99 fg: 2/48 bg: 3/944 fg/bg: 13.1 unadjusted p-value: 2.1e-002
    sequence logo of motif



  • DEBUGGING INFORMATION

    Command line:

    momo motifx --oc results/momo13 --db-background --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
    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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