Title: ASFinder: a tool for genome-wide identification of alternatively splicing transcripts from EST-derived sequences

Authors: Xiang Jia Min

Addresses: Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA

Abstract: Expressed Sequence Tags (ESTs) are a rich resource for identifying Alternatively Splicing (AS) genes. The ASFinder webserver is designed to identify AS isoforms from EST-derived sequences. Two approaches are implemented in ASFinder. If no genomic sequences are provided, the server performs a local BLASTN to identify AS isoforms from ESTs having both ends aligned but an internal segment unaligned. Otherwise, ASFinder uses SIM4 to map ESTs to the genome, then the overlapping ESTs that are mapped to the same genomic locus and have internal variable exon/intron boundaries are identified as AS isoforms. The tool is available at http://proteomics.ysu.edu/tools/ASFinder.html.

Keywords: alternative splicing; alternatively splicing genes; cDNA; genomic sequences; genome mapping; expressed sequence tags; ESTs; bioinformatics; alternatively splicing isoforms.

DOI: 10.1504/IJBRA.2013.053603

International Journal of Bioinformatics Research and Applications, 2013 Vol.9 No.3, pp.221 - 226

Received: 08 Jan 2011
Accepted: 22 Mar 2011
Published online: 06 Sep 2014 *

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