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
msf
>file) and display all amino acids which match either a particular
sequence
>or a consensus sequence and display those as either dots or dashes
while
>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
