The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation

Background: Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method. However, integrated systems usually do not provide mechanisms to generate customized databases to predict particular protein functions. Here, we describe a tool termed PIPA (Pipeline for Protein Annotation) that has these capabilities. Results: PIPA annotates protein functions by combining the results of multiple programs and databases, such as InterPro and the Conserved Domains Database, into common Gene Ontology (GO) terms. The major algorithms implemented in PIPA are: (1) a profile database generation algorithm, which generates customized profile databases to predict particular protein functions, (2) an automated ontology mapping generation algorithm, which maps various classifi...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Chenggang Yu, Nela Zavaljevski, Valmik Desai, Seth Johnson, Fred J. Stevens, Jaques Reifman
• Keywords: Algorithm, BMCBI 2008, Database, Protein Functions