AGenDA: gene prediction by cross-species sequence comparison

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

Research output: Contribution to journalArticleResearchpeer-review

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

Fingerprint

Genes
Initiator Codon
Terminator Codon
Sequence Alignment
Statistical Models
Computational Biology
Sequence Analysis
Software

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

Cite this

Taher, L., Rinner, O., Garg, S., Sczyrba, A., & Morgenstern, B. (2004). AGenDA: gene prediction by cross-species sequence comparison. Nucleic acids research, 32(Web Server issue), W305-8. https://doi.org/10.1093/nar/gkh386

AGenDA : gene prediction by cross-species sequence comparison. / Taher, Leila; Rinner, Oliver; Garg, Saurabh; Sczyrba, Alexander; Morgenstern, Burkhard.

In: Nucleic acids research, Vol. 32, No. Web Server issue, 01.07.2004, p. W305-8.

Research output: Contribution to journalArticleResearchpeer-review

Taher, L, Rinner, O, Garg, S, Sczyrba, A & Morgenstern, B 2004, 'AGenDA: gene prediction by cross-species sequence comparison' Nucleic acids research, vol. 32, no. Web Server issue, pp. W305-8. https://doi.org/10.1093/nar/gkh386
Taher L, Rinner O, Garg S, Sczyrba A, Morgenstern B. AGenDA: gene prediction by cross-species sequence comparison. Nucleic acids research. 2004 Jul 1;32(Web Server issue):W305-8. https://doi.org/10.1093/nar/gkh386
Taher, Leila ; Rinner, Oliver ; Garg, Saurabh ; Sczyrba, Alexander ; Morgenstern, Burkhard. / AGenDA : gene prediction by cross-species sequence comparison. In: Nucleic acids research. 2004 ; Vol. 32, No. Web Server issue. pp. W305-8.
@article{56d801c7d4b649a1a2d6665e9870dbeb,
title = "AGenDA: gene prediction by cross-species sequence comparison",
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/.",
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",
author = "Leila Taher and Oliver Rinner and Saurabh Garg and Alexander Sczyrba and Burkhard Morgenstern",
year = "2004",
month = "7",
day = "1",
doi = "10.1093/nar/gkh386",
language = "English",
volume = "32",
pages = "W305--8",
journal = "Nucleic acids research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "Web Server issue",

}

TY - JOUR

T1 - AGenDA

T2 - gene prediction by cross-species sequence comparison

AU - Taher, Leila

AU - Rinner, Oliver

AU - Garg, Saurabh

AU - Sczyrba, Alexander

AU - Morgenstern, Burkhard

PY - 2004/7/1

Y1 - 2004/7/1

N2 - 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/.

AB - 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/.

KW - Animals

KW - Base Sequence

KW - Conserved Sequence

KW - DNA Footprinting

KW - Genes

KW - Genomics

KW - Humans

KW - Internet

KW - Mice

KW - Phylogeny

KW - RNA Splicing

KW - Sequence Alignment

KW - Sequence Analysis, DNA

KW - Sequence Homology, Nucleic Acid

KW - Software

U2 - 10.1093/nar/gkh386

DO - 10.1093/nar/gkh386

M3 - Article

VL - 32

SP - W305-8

JO - Nucleic acids research

JF - Nucleic acids research

SN - 0305-1048

IS - Web Server issue

ER -