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Short, Linear Motif Search SLiMSearch

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Allows motif consensus search, annotation and filtering. SLiMSearch is a web-based tool for the discovery of novel short linear motifs (SLiM) instances in a proteome. The framework searches characterized motif specificity determinants to identify putative novel motif instances which are annotated with accessibility information, evolutionary attributes and experimental information. The software can aid biologists in building hypotheses and designing experiments by simplifying the analysis of the functional and evolutionary features of motifs.

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SLiMSearch classification

  • Animals
    • Bos taurus
    • Caenorhabditis elegans
    • Danio rerio
    • Drosophila melanogaster
    • Gallus gallus
    • Homo sapiens
    • Mus musculus
    • Rattus norvegicus
    • Xenopus laevis
    • Xenopus tropicalis
  • Fungi
    • Candida albicans
    • Saccharomyces cerevisiae
    • Schizosaccharomyces pombe
  • Plants
    • Arabidopsis thaliana
  • Protists
    • Dictyostelium discoideum
    • Leishmania major
    • Plasmodium falciparum
    • Trichomonas vaginalis
  • Viruses

SLiMSearch specifications

Interface:
Web user interface
Input data:
A motif consensus describing the specificity determinants of a motif binding pocket and a species of interest.
Output data:
The consensus matches with overlapping feature and motif attribute annotations.
Computer skills:
Basic
Stability:
Stable
Restrictions to use:
None
Input format:
Motif regular expression.
Output format:
JSON or TDT
Version:
4.0
Maintained:
Yes

SLiMSearch support

Maintainer

  • Denis Shields <>

Credits

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Publications

Institution(s)

Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland; UCD School of Medicine & Medical Science, University College Dublin, Dublin, Ireland

Funding source(s)

Supported by a Science Foundation Ireland Starting Investigator Research Grant [13/SIRG/].

Link to literature

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