Orthology script

Script to predict orthologous sequences by reciprocal best hits. The script requires hmmer (hmmsearch) and ncbi-blast+ (blastdbcmd and blastp). Required input is a Pfam hmm profile, and two sets of sequences from different organisms. The hmm profile is used focus ortholog prediction for a Pfam family of sequences. <div><br></div><div>The first step of the analysis is to perform a hmmsearch using the given hmm profile against the set of sequences from organism A. Next, the sequences identified in the hmmsearch are used in a blastp search to identify hits in the set of sequences from organism B. Finally, the top hits are used in blastp searches against the sequences of organism A. The search results are printed in a tabulated format.