Applied Bioinformatics

, Volume 5, Issue 1, pp 49–53

BioParser

A Tool for Processing of Sequence Similarity Analysis Reports

Authors

  • Marcos Catanho
    • Department of Biochemistry and Molecular BiologyOswaldo Cruz Institute, Fiocruz
    • Department of GeneticsFernandes Figueira Institute, Fiocruz
  • Daniel Mascarenhas
    • Department of Biochemistry and Molecular BiologyOswaldo Cruz Institute, Fiocruz
  • Wim Degrave
    • Department of Biochemistry and Molecular BiologyOswaldo Cruz Institute, Fiocruz
    • Department of Biochemistry and Molecular BiologyOswaldo Cruz Institute, Fiocruz
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