BatchBLAST: A Java Software With Graphical User Interface To Blast Multiple Sequences Against Multiple Databases In Batch Mode

 

BLAST is a program package that searches sequence databases for related sequences and is among the most frequently used programs in biology.  In high-throughput molecular biology applications, it is often necessary to BLAST multiple query sequences against multiple sequence databases with concise output for easy reviewing. BatchBlast is a Java software developed for this purpose.  It allows users to do sequence search and analysis in a high throughput manner.  BatchBlast consists of three components: the intuitive graphical user interface where the user can specify the query sequence file and databases to BLAST against, the BLAST result parser to parse the BLAST result in free text format and the output generator to display the summarized BLAST results in HTML format for easy reviewing.  By taking advantage of Java multiple threading technologies, BatchBlast allows users to launch multiple BLAST searches at the same time.  Since BLAST search requires formatted databases, BatchBlast has the functionality for the user to make blastable databases as well.

 

Please click here to download BatchBLAST.

 

 

JAVA BLAST Parser

 

Although BLAST probably is the most popular molecular biology program and Java is a popular computer programming language, there has not been a BLAST parser in Java yet for parsing BLAST output. A Java BLAST parser was developed using JavaCC technology. A parser grammar was first written and then used to produce the Java parser program by JavaCC. This parser is different from the one in BioJava, which only parses the BLAST output file in XML.

To develop the java BLAST parser, Java compiler compiler [tm] (JavaCC[tm]) technology was used.  JavaCC [tm], available for free (https://javacc.dev.java.net/), is the most popular parser generator for use with Java applications. A parser generator is a tool reading a grammar specification and then transforms it to a Java program that can recognize matches to the grammar. It provides a Java language extension for specifying a programming language grammar. For more information about the JavaCC technology please refer to https://javacc.dev.java.net/.

 

Please click here to download the BLAST parser grammar file, the Java BLAST parser generated by JavaCC and the parser API document.