title: A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses.
abstract: Proteins harbor domains or short linear motifs, which facilitate their functions and interactions. Finding functional motifs in protein sequences could predict the putative cellular roles or characteristics of hypothetical proteins. In this study, we present Shetti-Motif, which is an interactive tool to (i) map UniProt and PROSITE flat files, (ii) search for multiple pre-defined consensus patterns or experimentally validated functional motifs in large datasets protein sequences (proteome-wide), (iii) search for motifs containing repeated residues (low-complexity regions, e.g., Leu-, SR-, PEST-rich motifs, etc.). As proof of principle, using this comparative proteomics pipeline, eleven proteomes encoded by member of Poxviridae family were searched against about 100 experimentally validated functional motifs. The closely related viruses and viruses infect the same host cells (e.g. vaccinia and variola viruses) show similar motif-containing proteins profile. The motifs encoded by these viruses are correlated, which explains why poxviruses are able to interact with wide range of host cells. In conclusion, this in silico analysis is useful to establish a dataset(s) or potential proteins for further investigation or compare between species.
authors.affiliation: Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden. haithamsobhy@gmail.com.
authors.forename: Haitham
authors.initials: H
authors.lastname: Sobhy
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics*; D000595:Amino Acid Sequence / Q000235:genetics; D019295:Computational Biology; D054884:Host-Pathogen Interactions / Q000235:genetics; D011212:Poxviridae / Q000235:genetics* / Q000472:pathogenicity; D000072417:Protein Domains / Q000235:genetics; D020543:Proteome / Q000235:genetics*
chemical_list: D020543:Proteome
keywords: Comparative genomics; Functional genomics; Low-complexity regions (LCRs); Protein annotation; Protein domain; Protein function