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
Mutations in these areas more likely to affect function.
Identification of conserved residues in proteins.
Prerequisite for doing phylogenetic trees.
Identification of conserved domains:
How MSAs are computed
You still may have to do some
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.