[ssml] Redundancy in MSA for building HMM

[Goel, Manisha]

Hi All,

I am trying to build Profile HMM for a couple of protein domain families
(as defined in SCOP).
For building a Multiple sequence alignment, I have picked up related
members from PDB, but since the PDB often contains many structures of
the same protein (with multiple ligands or so), my alignments have
multiple copies of the same/highly similar sequences. 
 
Will the high redundancy of such an alignment effect the HMM model
quality ?
Since I will not be using these HMMs to look for distant relationships
but only confine myself to studying the members within a family .. I was
assuming this should not be problem.
Any suggestions ?
 
Thanks,
-Manisha
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