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<h2>Generating ACT Comparison File</h2>
<p>BLAST is used to generate the ACT comparison file (for more details see the <a href="http://www.sanger.ac.uk/Software/ACT/">ACT manual</a>) one of the
sequences needs to be made the database sequence and indexed with formatdb:
</p><pre>formatdb -i NC_004314.fasta -p 'F'
</pre>
<p>The other sequence is the query and you can then search for matches between these:
</p>
<pre>blastall -p tblastx -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_tblastx -m 8
</pre><p>or
</p>
<pre>blastall -p blastn -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_blastn -m 8 -e 0.1
</pre>
<p>Use the '-m 8' option to provide the tabular output that ACT uses.
</p><p>An alternative to this is to use <a href="http://www.webact.org">WebACT</a> or <a href="http://www.hpa-bioinfotools.org.uk/pise/double_act.html">Double ACT</a> to generate the comparison file.
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