BlaSTorage: a fast package to parse, manage and store BLAST results
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Data
2013-01-30
Autori
Orsini, Massimiliano
Carcangiu, Simone
Titolo del periodico
ISSN
Titolo del volume
Editore
BioMed Central
Abstract
Background: Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to single results, and performing logical operations
over them.
Findings: We implemented BlaSTorage, a Python package that parses multi BLAST results and returns them in a purpose-built object-database format. Unlike other BLAST parsers, BlaSTorage retains and stores all parts of BLAST results, including alignments, without loss of information; a complete API allows access to all the data components.
Conclusions: BlaSTorage shows comparable speed of more basic parser written in compiled languages as C++ and can be easily integrated into web applications or software pipelines.
Descrizione
Keywords
BLAST , Blast parser , Python-package , Serialized python object