Protein Function Prediction: Methods and Protocols

Abstract

This book begins by introducing two sequence-based function prediction methods, PFP and ESG, in Chapter 1. The chapter also describes a web server, NaviGO, which can analyze Gene Ontology annotations. Then, Chapters 2, 3, and 4 discuss tools suitable for the functional analysis of metagenomics data. The tools in these three chapters are based on sequence database searches faster than conventional homology search methods, a necessity when processing the large amounts of sequence data which typify metagenome sequences. Chapter 2 introduces GhostX, which uses a suffix array for fast sequence comparison. Fun4Me in Chapter 3 is a pipeline that combines protein coding gene detection in query sequences and a fast sequence database search utilizing a hashing technique. SUPERFOCUS in Chapter 4 combines fast search algorithms with preclustered reference sequence databases. In Chapter 5, we have MPFit, a program that detects when query proteins are moonlighting proteins, i.e., a protein with dual functions.