Abstract
MotivationBLAST 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.ResultsWe 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:
Highlights
The NCBI BLAST database search tool is one of the most popular programs designed to solve single query problems
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 imported into any statistical package such as Excel or SPSS for further analysis
Summary
The application generates a tab delimited text file that can be imported into any statistical package such as Excel or SPSS for further analysis. For each BLAST hit, the program derives and saves the following features: Query ID, Query Length, Accession version and GI number, Alignment Length, Score, bit, E-value, Identities, Positives, Gaps, Frame, Organism, and Description. ▪ Identities Text: full text representation plus characters matching (e.g. 110/130 (90%)). ▪ Position Query: as text representation plus the length of the frame (e.g. 328–600 (360)). ▪ Position Subject: as text representation plus the length of the frame (e.g. 1–110 (120))
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