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Massaging sequence data

Keith James bss194 at pwilliams.bangor.ac.uk
Tue Jun 10 04:36:45 EST 1997

Matt Rockman <mrockman at pantheon.yale.edu> writes:

> I have a large matrix of aligned sequences and I'm analyzing it in a
> variety of ways. One approach I would like to try is parsimony excluding
> silent transitions. I have seen this done by 1) excluding all third
> position transversions and 2) recoding leucine codon first positions as R
> and Y. 
> My question is pretty simple and mechanical: is there any shortcut to
> recoding the leu first positions? My matrix is huge and I am not eager to
> sort through looking for leu codons and changing the first position. Does
> anybody know of a trick for doing this?

If you let me know the format of your matrix I could have a go at this
when I have some spare time. Chopping up a sequence in frame and doing
the substitution should be straightforward.

> (please respond by reply email)

Posted and mailed.
Keith James Ph.D. - k.james at bangor.ac.uk  PGP 2.6.2i  Key ID 469A9FA1
Biodegradation Group                         *Encrypt and Survive*  
School of Biological Sciences    Guvf znl znxr ab frafr vs bar bs gur
University of Wales, Bangor, UK  vasvavgr ahzore bs zbaxrlf vf bssyvar

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