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

Xiang Jia Min1

  • 1Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA. xmin@ysu.edu

International Journal of Bioinformatics Research and Applications
|May 8, 2013
PubMed
Summary

ASFinder is a webserver that identifies alternatively spliced (AS) genes from expressed sequence tags (ESTs). It uses BLASTN or SIM4 mapping to detect AS isoforms, aiding in gene discovery.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Expressed Sequence Tags (ESTs) are valuable for gene discovery.
  • Identifying alternatively spliced (AS) genes is crucial for understanding gene function diversity.

Purpose of the Study:

  • To present ASFinder, a webserver tool for identifying alternatively spliced (AS) isoforms from EST-derived sequences.
  • To provide two distinct computational approaches for AS isoform detection.

Main Methods:

  • ASFinder utilizes local BLASTN for ESTs with aligned ends and unaligned internal segments when genomic sequences are absent.
  • When genomic sequences are provided, ASFinder employs SIM4 to map ESTs, identifying overlapping ESTs with variable exon/intron boundaries as AS isoforms.

Main Results:

  • The ASFinder webserver effectively identifies alternatively spliced isoforms from EST data.
  • The tool offers two complementary methods for AS detection, adaptable to the availability of genomic sequences.

Conclusions:

  • ASFinder provides a user-friendly platform for discovering alternatively spliced genes from ESTs.
  • This tool facilitates research in transcriptomics and gene expression analysis.