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BioParser: a tool for processing of sequence similarity analysis reports.
Marcos Catanho1, Daniel Mascarenhas, Wim Degrave
1Department of Biochemistry and Molecular Biology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
Applied Bioinformatics
|March 17, 2006
Summary
BioParser is a Perl program that simplifies the analysis of large sequence similarity search reports from BLAST and FASTA. It efficiently filters, stores, and processes data, making large-scale bioinformatics analyses more manageable.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomic Data Analysis
Background:
- BLAST and FASTA searches generate extensive output, impractical for manual review with large datasets.
- Efficient parsing of sequence similarity reports is crucial for large-scale bioinformatics studies.
Purpose of the Study:
- To introduce BioParser, a Perl program designed to parse BLAST and FASTA reports.
- To facilitate the filtering, storage, and retrieval of information from sequence similarity searches.
- To enable automated data processing for large-scale similarity analyses.
Main Methods:
- BioParser utilizes the BioPerl toolkit for report parsing.
- The program filters and stores report components in ASCII or HTML formats.
- BioParser can populate a local MySQL database for further data manipulation.
Main Results:
- BioParser effectively parses BLAST and FASTA reports, extracting key information.
- The tool allows for filtering hits and alignments based on specific attributes.
- Automated database population streamlines data handling for extensive analyses.
Conclusions:
- BioParser is a valuable tool for large-scale similarity analyses.
- It improves access to and extraction of information from sequence alignment data.
- The program simplifies the handling and processing of large datasets in bioinformatics.
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