Commands used to build the plast_RRNA.hmm
hmmbuild --dna -n RRNA_23S --wpb plast_RRNA_23S.hmm 23S.goodali.fst
hmmbuild --dna -n RRNA_16S --wpb plast_RRNA_16S.hmm 16S.goodali.fst
hmmbuild --dna -n RRNA_5S --wpb plast_RRNA_5S.hmm 5S.goodali.fst
hmmbuild --dna -n RRNA_4.5S --wpb plast_RRNA_4.5S.hmm 4.5S.goodali.fst
revcomp 23S.goodali.fst > 23S.goodali.rc.fst
revcomp 16S.goodali.fst > 16S.goodali.rc.fst
revcomp 5S.goodali.fst > 5S.goodali.rc.fst
revcomp 4.5S.goodali.fst > 4.5S.goodali.rc.fst
hmmbuild --dna -n RRNA_23S_RC --wpb plast_RRNA_23S_RC.hmm 23S.goodali.rc.fst
hmmbuild --dna -n RRNA_16S_RC --wpb plast_RRNA_16S_RC.hmm 16S.goodali.rc.fst
hmmbuild --dna -n RRNA_5S_RC --wpb plast_RRNA_5S_RC.hmm 5S.goodali.rc.fst
hmmbuild --dna -n RRNA_4.5S_RC --wpb plast_RRNA_4.5S_RC.hmm 4.5S.goodali.rc.fst
cat plast_RRNA_*.hmm > plast_RRNA.hmm
#
# Command for mitochondrion rRNA models
#
splitgbk.sh mitochondrion.1.genomic.gbff
pushd mitochondrion
rm $(grep -H "^CONTIG" * | awk -F ":" '{print $1}')
popd
buildRRNAModels_mito.sh $(pwd)/mitochondrion/*.gbk
