 We provide a brief overview of the state of alignment and secondary structure prediction algorithms. This is followed by a step-by-step iterative protocol for identifying  homologs, then constructing an alignment and corresponding CM.
<clarity>  We provide a brief overview of the state of alignment and secondary structure prediction algorithms. This is followed by a step-by-step iterative protocol for identifying  homologs, then constructing an alignment and corresponding CM.
 We provide a step-by-step iterative protocol for identifying homologs, then constructing an alignment and corresponding CM.