[Bioperl-l] BLAST reports

Fairley, Derek Derek.Fairley at bll.n-i.nhs.uk
Wed Dec 13 05:00:16 EST 2006


Hi Keith,

>I would like to manipulate my blast results with bioperl but would also
>like to have the html output of the blast.  What would be the best way
>of going about this, as I don't see any write functions in any of the
>blast modules I have looked at.  Would it be better to create my own
>html layout from the blast data then attempt to recover this from bioperl?

Take a look at some of the example scripts here:
http://www.bioperl.org/wiki/Bioperl_scripts
Depending on your Bioperl installation, you may already have these in your /scripts directory or similar. The /examples/searchio/htmlwriter.pl script may be a good starting point.

>p.s. - does anyone know what the most informative blast "alignment view"
>output is? xml i suppose?

Assuming you want to get the HSPs, parsing blastxml reports seems to be the most reliable approach. Again, there's a useful script for this: take a look at /scripts/utilities/search2alnblocks.pls.

Derek.



-- 
 ><)))°> -cGRASP- <°(((><
 Keith Anthony Boroevich
 Davidson Lab
 Dept of Molecular Biology
 Simon Fraser University
 Tel: 604-268-7276

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