Tuesday, 19 June 2007

The SLiMDisc server: short, linear motif discovery in proteins

Davey NE*, Edwards RJ* & Shields DC (2007): The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res. 35(Web Server issue):W455-9. *Joint first authors


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/~slimdisc/.

PMID: 17576682

Friday, 1 June 2007

Evolution of specificity and diversity

Shields DC, Johnston CR, Wallace IM & Edwards RJ (2007): Evolution of specificity and diversity. In: Ancestral Sequence Reconstruction Edited by DH Ardell, DA Liberles, G Matassi. Oxford University Press.