AVATAR: a database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs

Fang Rong Hsu; Hwan-You Chang; Yaw-Lin Lin; Yin-Te Tsai; Hui-Ling Peng; Ying Tsong Chen; Chia Yang Cheng; Min Yao Shih; Chia-Hung Liu; Chin-Feng Chen

doi:10.6026/97320630001016

AVATAR: a database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs

Bioinformation. 2005 Apr 22;1(1):16-8. doi: 10.6026/97320630001016.

Authors

Fang Rong Hsu¹, Hwan-You Chang, Yaw-Lin Lin, Yin-Te Tsai, Hui-Ling Peng, Ying Tsong Chen, Chia Yang Cheng, Min Yao Shih, Chia-Hung Liu, Chin-Feng Chen

Affiliation

¹ Bioinformatics Research Center, Department of Information Engineering and Computer Science, Feng Chia University, Taiwan. frhsu@fcu.edu.tw

Abstract

In the past years, identification of alternative splicing (AS) variants 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: The database is available for free at http://avatar.iecs.fcu.edu.tw/