ProFAT: a web-based tool for the functional annotation of protein sequences

Background: The functional annotation of proteins relies on published information concerning their close and remote homologues in sequence databases. Evidence for remote sequence similarity can be further strengthened by a similar biological background of the query sequence and identified database sequences. However, few tools exist so far, that provide a means to include functional information in sequence database searches. Results: We present ProFAT, a web-based tool for the functional annotation of protein sequences based on remote sequence similarity. ProFAT combines sensitive sequence database search methods and a fold recognition algorithm with a simple text-mining approach. ProFAT extracts identified hits based on their biological background by keyword-mining of annotations, features and most importantly, literature associated with a sequence entry. A user-provided keyword list enables the user to specifically search for weak, but biologically relevant homologues of an input qu...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Charles Richard Bradshaw, Vineeth Surendranath, Bianca Habermann
• Keywords: BMCBI 2006, Database, Protein, Sequence Database