BLAST Linearizer
About
This script implements a lossless transformation of BLAST output by converting each multi-block alignment into a single block (example below). The result is easier to parse, easier to read on large display and occupies slightly less space, while still containing all information.
This tool was made by Kirill Kryukov in Saitou lab, NIG. I share it with the hope that it can be useful, but without any warranties.
This script was tested with the default pairwise output format (-outfmt 0) of blastn, blastx and tblastx from BLAST+ 2.2.25 package, and should probably work with any other version. Please report any issues or incompatibilities.
News
2012-01-12 – This page is created.
Download
(Distributed under the zlib/libpng license, see the source file for details)
Usage
perl blast_linearizer.pl <blastoutput.txt >linear.txt
You can also process BLAST output on the fly as it is generated. Simply append
| perl blast_linearizer.pl >linear.txt
to the end of your search command instead of specifying the output file.
Example
Input (fragment):