SLiMFinder beta 1.0

Description

SLiMFinder is a method to find shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner. Read more ...

Pages:

  • Manual
  • Download
  • Help
  • Input examples
    Uniprot
    		•
    View job


    Publications:

    Edwards RJ, Davey NE & Shields DC (2007): SLiMFinder: A probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS ONE 2(10): e967.

    Click here for full list of References and Citations

    Input options

    Protein sequence input file
    Enter 3+ protein sequences (max 10000 characters)

    Motif Options


    Motif Search Options
    minwild
    maxwild
    slimlen
    wildvar

    Occurence Options
    minocc
    absmin


    Ambiguity Options
    equiv
    preamb
    combamb

    SLiMBuild Options


    BLAST options
    blaste
    Masking Options
    compmask
    maskm

    Special Options
    alphahelix
    termini

    Output Options


    Options
    topranks
    minic
    probcut

    Motif Filtering Options
    musthave
    query

    Gopher Options

    usegopher
    Choose Search Database from Kingdom/Phyla/Class groupings
    embl_archaea
    embl_bacteria
    embl_euk_extra
    		 embl_fungi
    embl_insecta
    embl_metazoa
    		 embl_vertebrata
    embl_viridiplantae
    embl_viruses
    Choose Search Database from Ensembl Genomes
    AEDAE
    ANOGA
    BOVIN
    BRARE
    CAEEL
    CANFA
    		 CHICK
    CIOIN
    CIOSA
    DASNO
    DROME
    ECHTE
    		 FUGRU
    GASAC
    HUMAN
    LOXAF
    MACMU
    MONDO
    		 MOUSE
    PANTR
    RAT
    TETNG
    XENTR
    YEAST

    Alignment Options

    A
    R
    N
    D
    C
    Q
    E
    G
    H
    I
    L
    K
    M
    F
    P
    S
    T
    W
    Y
    V
    Choose amino acid colours for the alignments
    Norman Davey(2006)