BLAST Filter Tool

Introduction

This project contains a Java software implementing a tool capable of filtering NCBI BLAST results with user-defined constraints.

BLAST Filter Tool (BFT) contains:

the filtering engine to be used as a command-line tool
a graphical filter editor to create filters in a very straightforward way without the need to use any obscure query language

While first designed to handle NCBI BLAST results, BFT is also capable of working on INRIA PLAST results or any other software packages capable of producing XML data files conform to NCBI_BlastOutput.dtd.

Requirements

Use a Java Virtual Machine 1.7 (or above) from Oracle.

Not tested with any other JVM providers but Oracle... so there is no guarantee that the software will work as expected if not using Oracle's JVM.

Working with the binary release

The most easy way to use BLAST Filter Tool consists in downloading an official release. It is made of a single Java binary archive file:

blast-filter-tool-x.y.z.jar

It is available from this Github page: check [Releases] tab and download the latest release.

We invite all users to start working with that tool, as explained in the next section.

Notice for developers: this unique JAR file is absolutely not intended to be embedded within any other applications since it contains all the dependencies (third-party librairies) of BFT into a single large file. So, if you want to include BFT into some other softwares, start from its source code.

User manual

It is available in the Wiki of this project.

BFT: develop using an IDE or Ant

I use Eclipse for development purpose, so BFT can be imported in that IDE (see dependencies, below).

Otherwise, you can use any other Java IDE and/or work on the command-line: a 'build.xml' for Ant 1.7+ is provided.

License and dependencies

BFT itself is released under the GNU Affero General Public License, Version 3.0. AGPL

BFT depends on several thrid-party libraries as stated in the NOTICE.txt file provided with this project.

A short story of BLAST Filter Tool (2006-today)

BLAST Filter Tool was started on october 2006. It is a concrete implementation of the Hyper-Graph Explorer (HGE) data modeling and querying system applied on sequence data (DNA, RNA and proteins). For more information on HGE, check this project.

From 2007 to 2015, it was licensed to the company Korilog to become the core of the data modeling and querying system of two other softwares I designed: KoriBlast and ngKLAST.

Finally, when Korilog ceased its activities on June 2015, I decided to release BFT source code to the open source community. I think (I hope) it will be of general interest for the bioinformatics community since working with BLAST results remain a de facto standard task when analysing sequence data.

pgdurand/BLAST-Filter-Tool