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Title

AVATAR: A database for genome-wide alternative splicing event detection through analysis of large scale ESTs and mRNAs

 

Authors

Fang Rong Hsu*1, Hwan-You Chang2, Yaw-Lin Lin3, Yin-Te Tsai3, Hui-Ling Peng4, Ying Tsong Chen4, Chia Yang Cheng5, Min Yao Shih6, Chia-Hung Liu6, Chin-Feng Chen7

 

Affiliation

1Bioinformatics Research Center, Department of Information Engineering and Computer Science, Feng Chia University, Taiwan; 2Department of Life Science, National Tsing-Hua University, Hsin-chu, Taiwan; 3Department of Computer Science and Information Management, Providence University; 4Department of Biological Science and Technology, National Chiao-Tung University; 5Department of Computer Science, National Tsing-Hua University, Hsin-chu, Taiwan; 6Department of Binformatics, Taichung Healthcare & Management University; 7Department of Information Engineering, Taichung Healthcare & Management University; No. 100 Wenhwa Rd., Seatwen, Taichung, Taiwan 40724, R.O.C

 

E-mail*

frhsu@fcu.edu.tw; * Corresponding author

 

Article Type

 

Web database

 

Date

 

received April 15, 2005; revised April 20, 2005; accepted  April 20, 2005; published online April 22, 2005

 

Abstract

 

In the past years, the analysis of alternative splicing (AS) has been gaining momentum. We developed AVATAR, a database for documenting AS using 5,469,433 human EST sequences and 26,159 human mRNA sequences.  AVATAR contains 12000 alternative splicing sites identified by mapping ESTs and mRNAs with the whole human genome sequence. AVATAR also contains AS information for 6 eukaryotes. We mapped EST alignment information into a graph model where exons and introns are represented with vertices and edges, respectively. AVATAR can be queried using, (1) gene names, (2) number of identified AS events in a gene, (3) minimal number of ESTs supporting a splicing site, etc. as search parameters. The system provides visualized AS information for queried genes.

 

Availability

http://avatar.iecs.fcu.edu.tw/

 

Keywords

 

alternative splicing; EST; sequence alignment; mRNA; protein diversity; database; human; eukaryotes

 

Citation

 

Hsu et al., Bioinformation 1(1): 16-18 (2005)

 

Edited by

 

M. K. Sakharkar

 

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.