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Bioinformatics Advance Access published online on February 18, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti332
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 14, 2004
Revised January 29, 2005
Accepted February 14, 2005

Applications note

ESTviewer: a Web interface for visualizing mouse, rat, cattle, pig, and chicken conserved ESTs in human genes and human alternatively spliced variants

Feng-Chi Chen 1 and Trees-Juen Chuang 2*

1 Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; Institute of Information Science, Academia Sinica, Taipei 11529, Taiwan
2 Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan

* To whom correspondence should be addressed.
Trees-Juen Chuang, E-mail: trees{at}gate.sinica.edu.tw


  Abstract

Summary: ESTviewer is a Web application for interactively visualizing human gene structures, with emphasis on mammalian and avian ESTs that are conserved in the human genome and alternatively spliced (AS) variants. AS variants from the UCSC, Vega, and PSEP annotations are presented in this application for comparison. EST data from six species, including human, mouse, rat, cattle, pig, and chicken, are mapped to the human genome to show cross-species EST conservation in annotated exonic and intronic regions. Cross-species EST conservation is evolutionarily and functionally important because it represents the effects of selection pressure on genic regions and transcriptome over evolutionary time. Emphatically, ESTviewer provides a convenient tool to compare highly conserved non-human ESTs and human AS variants. The application takes human gene accession Ids or coordinates of genomic sequences as inputs and presents annotated gene structures and their AS variants. In addition, the lengths and percentages of human genic regions covered by ESTs are displayed to show the level of EST coverage of different species. The percentages of the UCSC, Vega, and PSEP annotated exons covered by ESTs of the six studied species are also displayed in the interface.

Availability: The ESTviewer Web interface is publicly accessible at http://gate.sinica.edu.tw/~trees/ESTviewer/ESTviewer.htm.

Supplementary information: Detailed documentation and the data sets, including the whole human genome annotation of PSEP and 6-species ESTs conserved in the human genome, can be found on the ESTviewer home page.


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