[Bioperl-l] needle parser in bioperl?

Fairley, Derek Derek.Fairley at bll.n-i.nhs.uk
Thu Dec 14 12:58:10 EST 2006



>From http://emboss.sourceforge.net/apps/cvs/needle.html:


"The results can be output in one of several styles by using the
command-line qualifier -aformat xxx, where 'xxx' is replaced by the name
of the required format. Some of the alignment formats can cope with an
unlimited number of sequences, while others are only for pairs of


The available multiple alignment format names are: unknown, multiple,
simple, fasta, msf, trace, srs 


The available pairwise alignment format names are: pair, markx0, markx1,
markx2, markx3, markx10, srspair, score 


See: http://emboss.sf.net/docs/themes/AlignFormats.html for further
information on alignment formats."


Not sure based on this whether you can get pairwise alignment in .msf
format; can't think of a good reason why not. The BioPerl Align::IO
module will allow you to parse alignments in .msf format.






-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of neeti somaiya
Sent: 14 December 2006 08:03
To: Chris Fields; bioperl-l
Subject: Re: [Bioperl-l] needle parser in bioperl?


How do I run needle specifying that I want the MSF format, on a linux

The help doesnt show me any format option. Is there anything available

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

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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