[EMBOSS] Help with stretcher

[michael watson (IAH-C)]

What I want to avoid is my smaller sequence being split up into multiple
"HSPs" that I then have to process... 

-----Original Message-----
From: Ryan Golhar [mailto:golharam at umdnj.edu] 
Sent: 02 November 2005 15:07
To: michael watson (IAH-C); emboss at emboss.open-bio.org
Subject: RE: [EMBOSS] Help with stretcher

>From what you are describing, it sounds like you should use water or
another local alignment program.


-----Original Message-----
From: emboss-bounces at emboss.open-bio.org
[mailto:emboss-bounces at emboss.open-bio.org] On Behalf Of michael watson
(IAH-C)
Sent: Wednesday, November 02, 2005 7:34 AM
To: emboss at emboss.open-bio.org
Subject: [EMBOSS] Help with stretcher


Hi

I am using stretcher from emboss in a perl script.  I am trying to
globally align a relatively short sequence with quite a long one.
Basically, the short one sits bang in the middle of the long one, with
almost 100% identity.  However, no matter how much I play with the
gaplength and gappenalty options, stretcher insists that the the first
base of the short sequence aligns with the first base of the long
sequence, followed by a HUGE gap in the alignment, followed by the rest
of the sequences, correctly aligned.  It's doing my nut in.

I'm using EMBOSS 2.9.0 on Suse Linux.

Any help?

Mick

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