SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions

The extensive intrinsically disordered regions of higher eukaryotic proteomes contain vast numbers of functional interaction modules known as short linear motifs (SLiMs). Here, we present SLiMSearch, a motif discovery tool that scans a motif consensus, representing the specificity determinants of a...

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Bibliographic Details
Published in:Nucleic acids research 2017-07, Vol.45 (W1), p.W464-W469
Main Authors: Krystkowiak, Izabella, Davey, Norman E
Format: Article
Language:English
Subjects:
Amino Acid Motifs
Animals
Arabidopsis - genetics
Arabidopsis - metabolism
Computational Biology - methods
Consensus Sequence
Evolution, Molecular
Gene Ontology
Humans
Internet
Intrinsically Disordered Proteins - chemistry
Intrinsically Disordered Proteins - genetics
Molecular Sequence Annotation - methods
Protein Interaction Domains and Motifs
Protein Processing, Post-Translational
Proteome - chemistry
Proteome - genetics
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae - metabolism
Sequence Alignment
Software
Web Server Issue
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Summary:The extensive intrinsically disordered regions of higher eukaryotic proteomes contain vast numbers of functional interaction modules known as short linear motifs (SLiMs). Here, we present SLiMSearch, a motif discovery tool that scans a motif consensus, representing the specificity determinants of a motif-binding domain, against a proteome to discover putative novel motif instances. SLiMSearch applies several distinct and complementary approaches exploiting the common properties of SLiMs to predict novel motifs. Consensus matches are annotated with overlapping sequence annotation, including feature information describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterisation of functional regions. Discriminatory motif attributes such as conservation and accessibility are also calculated. In addition, SLiMSearch provides functional enrichment and evolutionary analysis tools. The enrichment tool analyses GO terms, keywords and interacting partner enrichment to indicate possible motif function. The evolutionary tool evaluates motif taxonomic range and the conservation of motif sequence context. Consensus matches can be filtered based on motif attributes such as accessibility and taxonomic range; or by the localisation, interacting partners or ontology annotation of the peptide-containing protein. SLiMSearch supports a range of species of experimental and therapeutic relevance and is available online at http://slim.ucd.ie/slimsearch/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkx238