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AntiHunter: searching BLAST output for EST antisense transcripts.

Giovanni Lavorgna1, Luca Sessa, Alessandro Guffanti

  • 1Istituto Scientifico H. S. Raffaele, Via Olgettina 60, 20132 Milan, Italy. giovanni.lavorgna@hsr.it

Bioinformatics (Oxford, England)
|March 3, 2004
PubMed
Summary

AntiHunter is a new tool to identify expressed sequence tag (EST) antisense transcripts. It analyzes genomic sequences and transcript annotations to find potential antisense transcripts from BLAST results.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Identifying antisense transcripts is crucial for understanding gene regulation.
  • Existing methods for antisense transcript discovery can be complex or computationally intensive.

Purpose of the Study:

  • To introduce AntiHunter, a novel web-based tool for identifying expressed sequence tag (EST) antisense transcripts.
  • To provide researchers with an accessible platform for analyzing genomic data and discovering antisense transcripts.

Main Methods:

  • Users provide a genomic sequence and associated transcript annotations.
  • The tool masks repetitive genomic regions.
  • A BLASTN search is performed against a selected EST database.

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Main Results:

  • AntiHunter identifies putative antisense transcripts by comparing user-provided genomic data with EST databases.
  • The tool reports identified EST entries via email.

Conclusions:

  • AntiHunter offers an efficient and user-friendly approach for antisense transcript discovery.
  • This tool aids in the comprehensive analysis of gene expression and regulation.