Automatic annotation of protein motif function with Gene Ontology terms

Background: Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO) project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results: This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs a...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Xinghua Lu, Chengxiang Zhai, Vanathi Gopalakrishnan, Bruce G. Buchanan
• Keywords: BMCBI 2004, Protein, Protein Motifs, Protein Sequence Motifs