[Bioperl-l] needle parser in bioperl?

neeti somaiya neetisomaiya at gmail.com
Thu Dec 14 03:02:37 EST 2006

How do I run needle specifying that I want the MSF format, on a linux box?
The help doesnt show me any format option. Is there anything available to
pasre MSF format?
Please find an example alignment file attached. Here the seq_of_contig
aligns with the reference sequence (i.e. SEQ_1.REF) starting at position
(coordinate) 8918 of SEQ_1.REF. I basically want this coordinate from the
output alignment, how can I parse the result to get this?

On 12/12/06, Chris Fields <cjfields at uiuc.edu> wrote:
> On Dec 12, 2006, at 6:14 AM, neeti somaiya wrote:
> > Hi,
> >
> > Does anyone know of a bioperl parser for needle output, basically I
> > won't
> > where the target sequence aligns on the template (i.e. coordinate
> > on the
> > template where the taget aligns).
> >
> > --
> > -Neeti
> > Even my blood says, B positive
> I answered this a number of months back:
> http://tinyurl.com/yzlbx5
> 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'.
> chris

Even my blood says, B positive
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