AGenDA: gene prediction by cross-species sequence comparison.

B Morgenstern,S Garg,O Rinner,L Taher,A Sczyrba

doi:10.1093/nar/gkh386

Abstract

Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprinting: they exploit the fact that functionally important regions in genomic sequences are usually more conserved than non-functional regions. We created a WWW-based software program for homology-based gene prediction at BiBiServ (Bielefeld Bioinformatics Server). Our tool takes pairs of evolutionary related genomic sequences as input data, e.g. from human and mouse. The server runs CHAOS and DIALIGN to create an alignment of the input sequences and subsequently searches for conserved splicing signals and start/stop codons near regions of local sequence conservation. Genes are predicted based on local homology information and splice signals. The server returns predicted genes together with a graphical representation of the underlying alignment. The program is available at http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/.

Highlights

Accurate prediction of gene structures in raw genomic sequence data is a first and critical step in genome annotation.GENE PREDICTION BY CROSS-SPECIES SEQUENCE ALIGNMENTWith the increasing number of completely or partially sequenced genomes, an alternative approach to gene prediction hasThe online version of this article has been published under an open access model
These methods are based on the concept of phylogenetic footprinting: they exploit the fact that functionally important regions in genomic sequences are usually more conserved than non-functional regions
It is possible to identify genes by comparing evolutionary related genomic sequences to each other. This idea is based on the phylogenetic footprinting principle [5]: during evolution, functional regions of genomic sequences tend to be more conserved than non-functional regions

Summary

Introduction

Accurate prediction of gene structures in raw genomic sequence data is a first and critical step in genome annotation.GENE PREDICTION BY CROSS-SPECIES SEQUENCE ALIGNMENTWith the increasing number of completely or partially sequenced genomes, an alternative approach to gene prediction hasThe online version of this article has been published under an open access model. We created a WWW-based software program for homology-based gene prediction at BiBiServ (Bielefeld Bioinformatics Server). Our tool takes pairs of evolutionary related genomic sequences as input data, e.g. from human and mouse. The server runs CHAOS and DIALIGN to create an alignment of the input sequences and subsequently searches for conserved splicing signals and start/stop codons near regions of local sequence conservation.

Results

Conclusion