Modeling sequence and function similarity between proteins for protein functional annotation.

ABSTRACT: A common task in biological research is to predict function for proteins by comparing sequences between proteins of known and unknown function. This is often done using pair-wise sequence alignment algorithms (e.g. BLAST). A problem with this approach is the assumption of a simple equivalence between a minimum sequence similarity threshold and the function similarity between proteins. This assumption is based on the binary concept of homology in that proteins are or not homologous. The relationship between sequence and function however is more complex as well as pertinent for predicting protein function, e.g. evaluating BLAST alignments or developing training sets for profile models based on functional rather than homologous groupings. Our motivation for this study was to model sequ

SUBMITTER: Higdon R 

PROVIDER: S-EPMC4120521 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature