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Nucleic Acids Research 2006 34(Web Server issue):W280-W284; doi:10.1093/nar/gkl307
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

GeneAlign: a coding exon prediction tool based on phylogenetical comparisons

Shu Ju Hsieh1, Chun Yuan Lin2, Ning Han Liu1, Wei Yuan Chow2 and Chuan Yi Tang1,*

1 Department of Computer Science, National Tsing Hua University Hsinchu, Taiwan 300, ROC 2 Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University Hsinchu, Taiwan 300, ROC

*To whom correspondence should be addressed. Tel: 886 3 5731077; Fax: 886 3 5723694; Email: cytang{at}cs.nthu.edu.tw

Received February 14, 2006. Revised March 4, 2006. Accepted April 11, 2006.

GeneAlign is a coding exon prediction tool for predicting protein coding genes by measuring the homologies between a sequence of a genome and related sequences, which have been annotated, of other genomes. Identifying protein coding genes is one of most important tasks in newly sequenced genomes. With increasing numbers of gene annotations verified by experiments, it is feasible to identify genes in the newly sequenced genomes by comparing to annotated genes of phylogenetically close organisms. GeneAlign applies CORAL, a heuristic linear time alignment tool, to determine if regions flanked by the candidate signals (initiation codon-GT, AG-GT and AG-STOP codon) are similar to annotated coding exons. Employing the conservation of gene structures and sequence homologies between protein coding regions increases the prediction accuracy. GeneAlign was tested on Projector dataset of 491 human–mouse homologous sequence pairs. At the gene level, both the average sensitivity and the average specificity of GeneAlign are 81%, and they are larger than 96% at the exon level. The rates of missing exons and wrong exons are smaller than 1%. GeneAlign is a free tool available at http://genealign.hccvs.hc.edu.tw.


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