Before running ACT you will need to obtain a comparison file. ACT supports three different comparison file formats:
The output of BLAST version 2.2.2 or better. The blastall command must be run with the -m 8 flag which generates one line of information per HSP.
MEGABLAST output. ACT can also read the output of MEGABLAST, which is part of the blast distribution.
Anthony Underwood and Jonathan Green at the Health Protection Agency have developed an online tool, Double ACT, to generate ACT comparison files.
Also there is WebACT which was designed and built by James Abbott and David Aanensen at Imperial College, London and is hosted in the laboratory of Professor Brian Spratt at Imperial College London with funding from The Wellcome Trust.
At the Sanger Centre we generally use a perl script called big_blast.pl to run blast and generate a file of results in MSPcrunch format. To run this script you will need to install a copy of the Pathogen Sequencing Unit internal perl modules. big_blast.pl can also be used to process blast results after the fact with a command line like this:
big_blast.pl blast_results.out
Note that big_blast.pl has only been tested on UNIX and GNU/Linux machines.
Here is an example input file file generated by MSPcrunch -d.
1399 97.00 940 2539 sequence1.dna 1 1596 AF140550.seq
1033 93.00 9041 10501 sequence1.dna 9420 10880 AF140550.seq
828 95.00 6823 7890 sequence1.dna 7211 8276 AF140550.seq
773 94.00 2837 3841 sequence1.dna 2338 3342 AF140550.seq
The columns have the following meanings (in order): score, percent identity, match start in the query sequence, match end in the query sequence, query sequence name, subject sequence start, subject sequence end, subject sequence name.
The columns are separated by spaces.