[Bioperl-l] Bio::Tools::Run::Alignment::Probcons

[Albert Vilella]

Hi all,

I'm willing to add a Probcons wrapper/caller to bioperl, so that
probcons can be run as the other Bio::Tools::Run::Alignment::*
available.

http://probcons.stanford.edu/

I found that Probcons has a training "-t, --train FILENAME" option that
brings quite an improvement in the quality of the alignment. I haven't
been able to get the same results with Muscle v5 or v6. For example:

/home/avb/9_opl/probcons/probcons/probcons -ir 1000 -c 5 -pre 20 -e -t
CCO0757.fasta.aa.params CCO0757.fasta.aa

This gives a params file, that is used in the second round 
"-p, --paramfile FILENAME":

/home/avb/9_opl/probcons/probcons/probcons -ir 1000 -c 5 -pre 20 -p
CCO0757.fasta.aa.params CCO0757.fasta.aa

The resulting alignment is quite better than without using the "--train"
option.

I was wondering if the Bio::Tools::Run::Alignment should be aware of
this inside the module, or simply do these steps when calling (with
@params).

Any suggestion? Any other suggestions?

Looking forward to hearing from you,

Bests,

    Albert.