[EMBOSS] Help with stretcher

[Peter Rice]

michael watson (IAH-C) wrote:

> 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.

global alignemnts come ni two flavours - those that insist on aligning the 
entire length of both sequences (like stretcher) and those that allow gaps at 
the end without penalties (like needle). What you want depends on the 
sequences you are aligning (i.e. what the ends really mean)

You can simply use the needle program instead to get the results you want.

Stretcher was originally part of the FASTA package. We can look at adding an 
option for end weighting (and maybe making the default the same as for needle).

Hope that helps,

Peter