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Beyond Bioinformatics |
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Title |
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Comparative analysis of various gene finders specific to Caenorhabditis elegans genome
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Authors |
Luv Kashyap and Mohammad Tabish*
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Affiliation |
Department of Biochemistry, Faculty of Life Sciences, A. M. University, Aligarh, U.P. 202 002, India
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E-mail* |
tabish.biochem@gmail.com; * Corresponding author
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Phone |
+91-571-270-0741 and +91-98-371-08550
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Article Type |
Hypothesis
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Date |
received
July 26, 2006; revised September 12, 2006; accepted October 02,
2006; published online October 07, 2006 |
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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.
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Keywords
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gene prediction; multiple transcripts; exons, isoforms; C. elegans |
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Citation |
Kashyap & Tabish, Bioinformation 1(6): 203-207 (2006)
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Edited by |
P. Kangueane
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ISSN |
0973-2063
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Publisher |
Biomedical Informatics Publishing Group
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Copyright |
Publisher
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Copyright Transfer Statement |
The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.
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License |
This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
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