Multiple alignment of protein sequences

doelz at urz.unibas.ch doelz at urz.unibas.ch
Thu Feb 6 02:22:09 EST 1992


In article <1992Feb5.202309.22818 at coe.montana.edu>, umbjs at cs.montana.edu (Jean Starkey) writes:

> significant homology.  I have used FASTA and BESTFIT
> and other programs on the GCG package available on
> the front end of the Pittsburg super computer. 

If there is Version 7 of the GCG program software installed this 
contains the program PILEUP which gets you what you might need.
 
The question is just whether you're trying to align garbage or whether
there's really a piece of common information in it. No computer can help
if the desired homology doesn't exist. Unfourtunately, the computer 
won't tell you, but PILEUP will give up if you have more than 2000 Gap 
insertions. 

regards 
Reinhard 


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