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

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          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.

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          Most cited references4

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          NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results.

          NOBLAST (New Options for BLAST) is an open source program that provides a new user-friendly tabular output format for various NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn, Tblastx, Mega BLAST and Psi BLAST) without any use of a parser and provides E-value correction in case of use of segmented BLAST database. JAMBLAST using the NOBLAST output allows the user to manage, view and filter the BLAST hits using a number of selection criteria. A distribution package of NOBLAST and JAMBLAST including detailed installation procedure is freely available from http://sourceforge.net/projects/JAMBLAST/ and http://sourceforge.net/projects/NOBLAST. Supplementary data are available at Bioinformatics online.
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            Multi-query sequence BLAST output examination with MuSeqBox.

            MuSeqBox is a program to parse BLAST output and store attributes of BLAST hits in tabular form. The user can apply a number of selection criteria to filter out hits with particular attributes. MuSeqBox provides a powerful annotation tool for large sets of query sequences that are simultaneously compared against a database with any of the standard stand-alone or network-client BLAST programs. We discuss such application to the problem of annotation and analysis of EST collections. The program was written in standard C++ and is freely available to noncommercial users by request from the authors. The program is also available over the web at http://bioinformatics.iastate.edu/bioinformatics2go/mb/MuSeqBox.html.
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              • Record: found
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              Is Open Access

              Batch Blast Extractor: an automated blastx parser application

              Motivation BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time consuming, insufficient, and inaccurate. Therefore implementation of a parser application would be extremely useful in extracting information from BLAST outputs. Results We have developed a java application, Batch Blast Extractor, with a user friendly graphical interface to extract information from BLAST output. The application generates a tab delimited text file that can be easily imported into any statistical package such as Excel or SPSS for further analysis. For each BLAST hit, the program obtains and saves the essential features from the BLAST output file that would allow further analysis. The program was written in Java and therefore is OS independent. It works on both Windows and Linux OS with java 1.4 and higher. It is freely available from:
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                Author and article information

                Journal
                Source Code Biol Med
                Source Code Biol Med
                Source Code for Biology and Medicine
                BioMed Central
                1751-0473
                2013
                30 January 2013
                : 8
                : 4
                Affiliations
                [1 ]CRS4, Bioinformatics Group, Loc Pixina Manna, Pula 09010, ITALY
                Article
                1751-0473-8-4
                10.1186/1751-0473-8-4
                3571973
                23363699
                100cfac0-9a16-44f6-82bf-f19222fa4512
                Copyright ©2013 Orsini and Carcangiu; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 3 March 2012
                : 29 January 2013
                Categories
                Brief Reports

                Bioinformatics & Computational biology
                blast,blast parser,python-package,serialized python object

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