{"title":"BlaSTorage: a fast package to parse, manage and store BLAST results.","authors":"Massimiliano Orsini, Simone Carcangiu","doi":"10.1186/1751-0473-8-4","DOIUrl":null,"url":null,"abstract":"<p><strong>Unlabelled: </strong></p><p><strong>Background: </strong>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.</p><p><strong>Findings: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":"8 1","pages":"4"},"PeriodicalIF":0.0000,"publicationDate":"2013-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1751-0473-8-4","citationCount":"2","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Source Code for Biology and Medicine","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1186/1751-0473-8-4","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"Decision Sciences","Score":null,"Total":0}
引用次数: 2
Abstract
Unlabelled:
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.
期刊介绍：
Source Code for Biology and Medicine is a peer-reviewed open access, online journal that publishes articles on source code employed over a wide range of applications in biology and medicine. The journal"s aim is to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.
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