Skip Navigation

This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (25)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Morgenstern, B.
Right arrow Articles by Mewes, H.-W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Morgenstern, B.
Right arrow Articles by Mewes, H.-W.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 18 no. 6 2002
Pages 777-787
© 2002 Oxford University Press

Exon discovery by genomic sequence alignment

Burkhard Morgenstern 1,*, Oliver Rinner 2, Saïd Abdeddaïm 3, Dirk Haase 1, Klaus F. X. Mayer 1, Andreas W. M. Dress 4 and Hans-Werner Mewes 1

1 GSF Research Center, MIPS/Institute of Bioinformatics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
2 Physiologisch-Chemisches Institut, Universität Tübingen, Hoppe-Seyler-Straße 4, 72076 Tübingen, Germany
3 LIFAR-ABISS, Faculté des Sciences et Techniques, Université de Rouen, 76821 Mont-Saint-Aignan Cedex, France
4 Research Center for Interdisciplinary Studies on Structure Formation (FSPM), Universität Bielefeld, Postfach 100131, 33501, Bielefeld, Germany

Received on July 4, 2001 ; revised on October 24, 2001 and December 10, 2001 ; accepted on December 20, 2001

Motivation: During evolution, functional regions in genomic sequences tend to be more highly conserved than randomly mutating ‘junk DNA’ so local sequence similarity often indicates biological functionality. This fact can be used to identify functional elements in large eukaryotic DNA sequences by cross-species sequence comparison. In recent years, several gene-prediction methods have been proposed that work by comparing anonymous genomic sequences, for example from human and mouse. The main advantage of these methods is that they are based on simple and generally applicable measures of (local) sequence similarity; unlike standard gene-finding approaches they do not depend on species-specific training data or on the presence of cognate genes in data bases. As all comparative sequence-analysis methods, the new comparative gene-finding approaches critically rely on the quality of the underlying sequence alignments.

Results: Herein, we describe a new implementation of the sequence-alignment program DIALIGN that has been developed for alignment of large genomic sequences. We compare our method to the alignment programs PipMaker, WABA and BLAST and we show that local similarities identified by these programs are highly correlated to protein-coding regions. In our test runs, PipMaker was the most sensitive method while DIALIGN was most specific.

Availability: The program is downloadable from the DIALIGN home page at http://bibiserv.techfak.uni-bielefeld.de/dialign/

Contact: burkhard{at}TechFak.Uni-Bielefeld.DE

* To whom correspondence should be addressed at Universität Bielefeld, Technische Fakultät, Praktische Informatik, Postfach 100131, 33501 Bielefeld, Germany.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
A. Lomsadze, V. Ter-Hovhannisyan, Y. O. Chernoff, and M. Borodovsky
Gene identification in novel eukaryotic genomes by self-training algorithm
Nucleic Acids Res., November 28, 2005; 33(20): 6494 - 6506.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Pohler, N. Werner, R. Steinkamp, and B. Morgenstern
Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W532 - W534.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
B. Morgenstern, N. Werner, S. J. Prohaska, R. Steinkamp, I. Schneider, A. R. Subramanian, P. F. Stadler, and J. Weyer-Menkhoff
Multiple sequence alignment with user-defined constraints at GOBICS
Bioinformatics, April 1, 2005; 21(7): 1271 - 1273.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Morgenstern
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W33 - W36.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Brudno, R. Steinkamp, and B. Morgenstern
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W41 - W44.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Taher, O. Rinner, S. Garg, A. Sczyrba, and B. Morgenstern
AGenDA: gene prediction by cross-species sequence comparison
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W305 - W308.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Stanke, R. Steinkamp, S. Waack, and B. Morgenstern
AUGUSTUS: a web server for gene finding in eukaryotes
Nucleic Acids Res., July 1, 2004; 32(suppl_2): W309 - W312.
[Abstract] [Full Text] [PDF]

Home page
 J. Nutr.Home page
Y. Wang, B. Jones Voy, S. Urs, S. Kim, M. Soltani-Bejnood, N. Quigley, Y.-R. Heo, M. Standridge, B. Andersen, M. Dhar, et al.
The Human Fatty Acid Synthase Gene and De Novo Lipogenesis Are Coordinately Regulated in Human Adipose Tissue
J. Nutr., May 1, 2004; 134(5): 1032 - 1038.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. E. Moore and J. A. Lake
Gene structure prediction in syntenic DNA segments
Nucleic Acids Res., December 15, 2003; 31(24): 7271 - 7279.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. C.-C. Shih and W.-H. Li
GS-Aligner: A Novel Tool for Aligning Genomic Sequences Using Bit-Level Operations
Mol. Biol. Evol., August 1, 2003; 20(8): 1299 - 1309.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Dieterich, H. Wang, K. Rateitschak, H. Luz, and M. Vingron
CORG: a database for COmparative Regulatory Genomics
Nucleic Acids Res., January 1, 2003; 31(1): 55 - 57.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
W. M. Karlowski, H. Schoof, V. Janakiraman, V. Stuempflen, and K. F. X. Mayer
MOsDB: an integrated information resource for rice genomics
Nucleic Acids Res., January 1, 2003; 31(1): 190 - 192.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
N. Bray, I. Dubchak, and L. Pachter
AVID: A Global Alignment Program
Genome Res., January 1, 2003; 13(1): 97 - 102.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.