BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation

Background: Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence database searching and operon analysis. Other methods can support these techniques: We have developed an automatic method "BrEPS" that creates highly specific sequence patterns for the functional annotation of enzymes. Results: The enzymes in the UniprotKB are identified and their sequences compared against each other with BLAST. The enzymes are then clustered into a number of trees, where each tree node is associated with a set of EC-numbers. The enzyme sequences in the tree nodes are aligned with ClustalW. The conserved columns of the resulting multiple alignments are used to construct sequence patterns. In the last step, we verify the quality of the patterns by computing their specificity. Patterns with low specificity are omitted and recomputed further down ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Constantin Bannert, A. Welfle, C. aus dem Spring, Dietmar Schomburg
• Keywords: BMCBI 2010, Business, Enzymes, Functional Annotation, Sequence Patterns