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

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

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.