AGenDA: gene prediction by cross-species sequence comparison

Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Burkhard Morgenstern

Research output: Contribution to journalArticle

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/.

Original languageEnglish
Pages (from-to)W305-8
JournalNucleic acids research
Volume32
Issue numberWeb Server issue
DOIs
Publication statusPublished - 1 Jul 2004

Keywords

  • Animals
  • Base Sequence
  • Conserved Sequence
  • DNA Footprinting
  • Genes
  • Genomics
  • Humans
  • Internet
  • Mice
  • Phylogeny
  • RNA Splicing
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid
  • Software

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