Paralogous vs. orthologous sequence conservation

David Matthes dmatthes at email.sjsu.edu
Mon Nov 4 22:08:15 EST 2002


         Reply to:   Paralogous vs. orthologous sequence conservation
Anyone know of a simple way to accomplish the following?

Annotate a given protein sequence (say, human Glypican-3) to reflect which amino acids are conserved by one group of homologs (say, Glypican-3 sequences in mouse, rat, puffer fish [orthologs])  BUT NOT in another group of homologs (say, the other human glypicans [paralogs]).  The idea would be to have a very quick way to present the "family defining" amino acids common to a protein family separately from those "ortholog-defining" amino acids.  
Of course making a large MSA containing both sets of sequences would be a start, but that doesn't let one produce the simple output of a color-annotated *single* sequence (e.g. Glypican-3) where amino acids are highlighted increasingly red as they are conserved in one set and not the other, increasingly green as they are conserved in the second but not the first, and more yellow the closer they are to being conserved equally in both sets.  
If this can be done with existing applications, please let me know.  If not, can anyone see any reason why such an application wouldn't be helpful?  It seems to me that it would a relatively easy program to write and one with a significant utility for we who are biologists.




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