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<TITLE>Redundancy in MSA for building HMM</TITLE>
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<P><FONT SIZE=2 FACE="Arial">Hi All,</FONT>
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<P><FONT SIZE=2 FACE="Arial">I am trying to build Profile HMM for a couple of protein domain families (as defined in SCOP).</FONT>
<BR><FONT SIZE=2 FACE="Arial">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. </FONT></P>
<P><FONT SIZE=2 FACE="Arial"> </FONT>
<BR><FONT SIZE=2 FACE="Arial">Will the high redundancy of such an alignment effect the HMM model quality ?</FONT>
<BR><FONT SIZE=2 FACE="Arial">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.</FONT></P>
<P><FONT SIZE=2 FACE="Arial">Any suggestions ?</FONT>
<BR><FONT SIZE=2 FACE="Arial"> </FONT>
<BR><FONT SIZE=2 FACE="Arial">Thanks,</FONT>
<BR><FONT SIZE=2 FACE="Arial">-Manisha</FONT>
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