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 (14)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Novichkov, P. S.
Right arrow Articles by Mironov, A. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Novichkov, P. S.
Right arrow Articles by Mironov, A. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics Vol. 17 no. 11 2001
Pages 1011-1018
© 2001 Oxford University Press

Gene recognition in eukaryotic DNA by comparison of genomic sequences

P. S. Novichkov , M. S. Gelfand * and A. A. Mironov

State Scientific Center GosNIIGenetika, 1 Dorozhny pr. 1, Moscow 113545, Russia

Received on December 18, 2000 ; revised on April 9, 2001 ; accepted on July 25, 2001

Motivation: Sequencing of complete eukaryotic genomes and large syntenic fragments of genomes makes it possible to apply genomic comparison for gene recognition.

Results: This paper describes a spliced alignment algorithm that aligns candidate exon chains of two homologous genomic sequence fragments from different species. The algorithm is implemented in Pro-Gen software. Unlike other algorithms, Pro-Gen does not assume conservation of the exon–intron structure. Amino acid sequences obtained by the formal translation of candidate exons are aligned instead of nucleotide sequences, which allows for distant comparisons. The algorithm was tested on a sample of human–mammal (mouse), human–vertebrate (Xenopus ) and human–invertebrate (Drosophila ) gene pairs. Surprisingly, the best results, 97–98% correlation between the actual and predicted genes, were obtained for more distant comparisons, whereas the correlation on the human–mouse sample was only 93%. The latter value increases to 95% if conservation of the exon–intron structure is assumed. This is caused by a large amount of sequence conservation in non-coding regions of the human and mouse genes probably due to regulatory elements.

Availaility: Pro-Gen v. 3.0 is available to academic researchers free of charge at http://www.anchorgen.com/pro_gen/pro_gen.html.

Contact: misha{at}imb.imb.ac.ru

* To whom correspondence should be addressed.


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
 BioinformaticsHome page
W. H. Majoros, M. Pertea, and S. L. Salzberg
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding
Bioinformatics, May 1, 2005; 21(9): 1782 - 1788.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. D. Wu and C. K. Watanabe
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics, May 1, 2005; 21(9): 1859 - 1875.
[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
I. M. Meyer and R. Durbin
Gene structure conservation aids similarity based gene prediction
Nucleic Acids Res., February 4, 2004; 32(2): 776 - 783.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Foissac, P. Bardou, A. Moisan, M.-J. Cros, and T. Schiex
EUGENE'HOM: a generic similarity-based gene finder using multiple homologous sequences
Nucleic Acids Res., July 1, 2003; 31(13): 3742 - 3745.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Mathe, M.-F. Sagot, T. Schiex, and P. Rouze
Current methods of gene prediction, their strengths and weaknesses
Nucleic Acids Res., October 1, 2002; 30(19): 4103 - 4117.
[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.