[Bioperl-l] needle parser in bioperl?
cjfields at uiuc.edu
Tue Dec 12 11:57:27 EST 2006
On Dec 12, 2006, at 6:14 AM, neeti somaiya wrote:
> Does anyone know of a bioperl parser for needle output, basically I
> where the target sequence aligns on the template (i.e. coordinate
> on the
> template where the taget aligns).
> Even my blood says, B positive
I answered this a number of months back:
Basically, newer versions of EMBOSS have changed the output for the
AlignIO::emboss parser (which parses needle). I don't believe the
parser has been fixed to deal with that, but Jason has pointed out
you can use MSF output when running needle, then parse using AlignIO
with the format set to 'msf'.
More information about the Bioperl-l