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This article is part of the supplement: IEEE 7th International Conference on Bioinformatics and Bioengineering at Harvard Medical School

Open Access Research

Batch Blast Extractor: an automated blastx parser application

Mehdi Pirooznia1, Edward J Perkins2 and Youping Deng1*

Author Affiliations

1 Department of Biological Sciences, University of Southern MS, Hattiesburg, 39406, USA

2 Environmental Laboratory, U.S. Army Engineer Research and Development Center, 3909 Halls Ferry Rd, Vicksburg, MS, 39180, USA

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BMC Genomics 2008, 9(Suppl 2):S10  doi:10.1186/1471-2164-9-S2-S10

Published: 16 September 2008

Abstract

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: http://mcbc.usm.edu/BatchBlastExtractor/ webcite