HMMer-scripts

Scripts that deal with HMMer output

Scan protein sequences, predicted by Prokka 1.8, against a profile-HMM database (from Pfam in this case)

for i in *.faa; do hmmscan --cpu 4 --domtblout $i.hmm Pfam-A.hmm $i > $i.log; done

Only select genes that contain a functional domain or motif. The output is a GFF3 file that only stores domain containing genes

  perl extract_genes_with_domain.pl <hmm file from hmmscan> <prokka gff3 file>