[EMBOSS] Pairwise matching

[Henrikki Almusa]

Hi,

I'm doing pairwise matching with strecher on nucleotide sequences. From 
the limited testing it seems that the strecher will only match sequence 
I give it and not do the same match to other strand. Is this correct or 
have I mistaken the result?

There is an option '-sreverse' of course but that would change all input 
to other strand. I have a wrapper script around strecher which allows me 
to run the program for each pair of inputs (eg. from file 1 seq 1 
against file 2 seq and file 1 seq 2 against file 2 seq 2 and so on).

What would be preferable way to do local pairwise matching so that it 
would check the other strand as well and return the best match found? I 
suppose I could do it twice. Once for current strand and once for other 
and select best of each pair, but that would require more scripting to 
select the better result from the two files for each alignment.

Regards,
-- 
Henrikki Almusa