IUBio

protein alignment display

mathog at seqaxp.bio.caltech.edu mathog at seqaxp.bio.caltech.edu
Mon Feb 19 12:19:11 EST 1996


In article <4g2gc0$1emc at bigblue.oit.unc.edu>, ewb at med.unc.edu (Edward W. Baptist) writes:
>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?

If you have GCG MSF format then you presumably also have GCG, so consider
the GCG program PRETTY.  It has these command line options:

 IDEntity[=*]      only shows positions of unanimous agreement in the
                         consensus
 DIFferences[="-"] only shows positions disagreeing with the calculated
                         consensus

If EGCG is installed at your site PRETTYPLOT also has a "DIFferences="
switch, and BOXSHADE has "IDENTity" and "SIMilar" switches (only box amino
acids identical or similar to consensus).

Regards,

David Mathog
mathog at seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 




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