29 lines
1.0 KiB
Plaintext
29 lines
1.0 KiB
Plaintext
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 |