Title

Comparative analysis of various gene finders specific Caenorhabditis elegans genome

Authors

Luv Kashyap and Mohammad Tabish*

Affiliation

Department of Biochemistry, Faculty of Life Sciences, A. M. University, Aligarh, U.P. 202 002, India

E-mail*

tabish.biochem@gmail.com; * Corresponding author

Phone

+91-571-270-0741 and +91-98-371-08550

Article Type

Hypothesis

Date

received July 26, 2006; revised September 12, 2006; accepted October 02, 2006; published online October 07, 2006
 

Abstract

Computational gene prediction and identifying alternatively spliced isoforms have always been a challenging task. In this paper, we describe the performance of three gene/exon finding programmes namely Fex, Gen view2 and Gene builder capable of predicting open reading frames or exons for a given set of sequences from C. elegans genome. The predicted exons were compared with the ‘sequencing consortium’ identified exons and degree of consensus among them is discussed. We found that exon prediction by Fex was similar to the consortium prediction as compared to Gen view2 and Gene builder results. Interestingly, some exons (six exons in five genes) predicted positive only by Fex and not by the ‘sequencing consortium’ are found at the C. elegans EST database. This data is critical for further debate and discussion on gene finding in C. elegans.

Keywords

gene prediction; multiple transcripts; exons, isoforms; C. elegans

Citation

Kashyap & Tabish, Bioinformation 1(6): 203-207 (2006)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.