Applied Bioinformatics

, Volume 5, Issue 1, pp 49–53

BioParser

A Tool for Processing of Sequence Similarity Analysis Reports
  • Marcos Catanho
  • Daniel Mascarenhas
  • Wim Degrave
  • Antonio Basílio de Miranda
Application Note

DOI: 10.2165/00822942-200605010-00007

Cite this article as:
Catanho, M., Mascarenhas, D., Degrave, W. et al. Appl-Bioinformatics (2006) 5: 49. doi:10.2165/00822942-200605010-00007

Abstract

The widely used programs BLAST (in this article, ‘BLAST’ includes both the National Center for Biotechnology Information [NCBI] BLAST® and the Washington University version WU BLAST) and FASTA for similarity searches in nucleotide and protein databases usually result in copious output. However, when large query sets are used, human inspection rapidly becomes impractical. BioParser is a Perl program for parsing BLAST and FASTA reports. Making extensive use of the BioPerl toolkit, the program filters, stores and returns components of these reports in either ASCII or HTML format. BioParser is also capable of automatically feeding a local MySQL® database with the parsed information, allowing subsequent filtering of hits and/or alignments with specific attributes. For this reason, BioParser is a valuable tool for large-scale similarity analyses by improving the access to the information present in BLAST or FASTA reports, facilitating extraction of useful information of large sets of sequence alignments, and allowing for easy handling and processing of the data.

Copyright information

© Adis Data Information BV 2006

Authors and Affiliations

  • Marcos Catanho
    • 1
    • 2
  • Daniel Mascarenhas
    • 1
  • Wim Degrave
    • 1
  • Antonio Basílio de Miranda
    • 1
  1. 1.Department of Biochemistry and Molecular BiologyOswaldo Cruz Institute, FiocruzRio de JaneiroBrazil
  2. 2.Department of GeneticsFernandes Figueira Institute, FiocruzRio de JaneiroBrazil
  3. 3.Departamento de Bioquímica e Biologia MolecularFundação Oswaldo CruzRio de JaneiroBrazil