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BlaSTorage: a fast package to parse, manage and store BLAST results

Massimiliano Orsini* and Simone Carcangiu

Author Affiliations

CRS4, Bioinformatics Group, Loc Pixina Manna, Pula 09010, ITALY

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Source Code for Biology and Medicine 2013, 8:4  doi:10.1186/1751-0473-8-4

Published: 30 January 2013

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.

Keywords:
BLAST; Blast parser; Python-package; Serialized python object