Skip to main content
Article thumbnail
Location of Repository

The SLiMDisc server: short, linear motif discovery in proteins

By Norman E. Davey, Richard J. Edwards and Denis C. Shields

Abstract

Short, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein-protein interactions. Overrepresentation of convergent occurrences of motifs in proteins with a common attribute (such as similar subcellular location or a shared interaction partner) provides a feasible means to discover novel occurrences computationally. The SLiMDisc (Short, Linear Motif Discovery) web server corrects for common ancestry in describing shared motifs, concentrating on the convergently evolved motifs. The server returns a listing of the most interesting motifs found within unmasked regions, ranked according to an information content-based scoring scheme. It allows interactive input masking, according to various criteria. Scoring allows for evolutionary relationships in the data sets through treatment of BLAST local alignments. Alongside this ranked list, visualizations of the results improve understanding of the context of suggested motifs, helping to identify true motifs of interest. These visualizations include alignments of motif occurrences, alignments of motifs and their homologues and a visual schematic of the top-ranked motifs. Additional options for filtering and/or re-ranking motifs further permit the user to focus on motifs with desired attributes. Returned motifs can also be compared with known SLiMs from the literature. SLiMDisc is available at: http://bioware.ucd.ie/ approximately slimdisc/

Year: 2007
OAI identifier: oai:eprints.soton.ac.uk:143463
Provided by: e-Prints Soton

Suggested articles

Citations

  1. (1989). A conserved tripeptide sorts proteins to peroxisomes. doi
  2. (1990). Basic local alignment search tool. doi
  3. (1998). Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. doi
  4. (2006). DILIMOT: discovery of linear motifs in proteins. doi
  5. (2003). ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. doi
  6. (2005). IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. doi
  7. (2005). Linear motifs: evolutionary interaction switches. doi
  8. (2006). Minimotif Miner: a tool for investigating protein function. doi
  9. (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
  10. (2006). Peptides mediating interaction networks: new leads at last. doi
  11. (2006). SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. doi
  12. (2005). Systematic discovery of new recognition peptides mediating protein interaction networks. doi
  13. (2006). The Gene Ontology (GO) project in 2006. doi
  14. (2005). The Universal Protein Resource (UniProt).
  15. (2007). Vol. 35,Web Server issue W459 a t U n i v e r s i t y o f S o u t h a m p t o n o n A p r i l , h t t p : / / n a r . o x f o r d j o u r n a l s . o r g D o w n l o a d e d f r o m doi

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.