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					Multiple Sequence Alignments
                       Why Do MSAs?
   Although BLAST may give you good E-value – MSA more convincing
    that protein is related and can be aligned over entire length.

   Identification of conserved regions or domains in proteins.
        Regions that are evolutionary conserved are likely to be important for
         structure/function.
        Mutations in these areas more likely to affect function.


   Identification of conserved residues in proteins.

   Prerequisite for doing phylogenetic trees.
Identification of conserved domains:
Human b-defensins
How MSAs are computed
You still may have to do some
         hand-editing!!
           T-Coffee Vs Clustal

   ClustalW is standard program for MSAs.

   However, new program T-Cofffee often
    does a better job particularly with more
    distantly related proteins.

				
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posted:12/19/2011
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