protein alignment display

a michael.baron
Mon Feb 19 05:36:24 EST 1996

In article <4g2gc0$1emc at bigblue.oit.unc.edu>, ewb at med.unc.edu (Edward W. 
Baptist) says:
>Is there a program which will take a protein alignment (such as a GCG 
>file) and display all amino acids which match either a particular 
>or a consensus sequence and display those  as either dots or dashes 
>printing out only the ones that differ?

The program BOXSHADE has an ASCII output option that will do what you 
want. You have to specify one of the input sequences as the 'master' 
sequence, and the others are compared to that. Matching sequences can be 
shown/printed in a different case/replaced with dots, as required.
The program is available from the EMBL software archive.

Michael Baron

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