AVATAR: a database for genome-wide alternative splicing event detection using large scale ESTs and mRNAs |
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| Authors: | Hsu Fang Rong Chang Hwan-You Lin Yaw-Lin Tsai Yin-Te Peng Hui-Ling Chen Ying Tsong Cheng Chia Yang Shih Min Yao Liu Chia-Hung Chen Chin-Feng |
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| Institution: | Bioinformatics Research Center, Department of Information Engineering and Computer Science, Feng Chia University, Taiwan. frhsu@fcu.edu.tw |
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| 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 |
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