Loading page2.Rmd +6 −5 Original line number Diff line number Diff line Loading @@ -2,15 +2,16 @@ title: Profile-HMM of coronavirus sequence --- # Solution using hmmer # Expects you have obtained data (explained on page1), expects aligned sequences ```bash apt get hmmer pip3 install pyfasta pyfasta split --header "fff/%(seqid)s.fasta" all.fasta hmmbuild MN908947.hmm MN908947.fasta hmmbuild output.hmm input_sequence.fasta ``` #(repeat for each sequence all call for all files in directory using bash command) # Another possible solution # Another possible solution in r # large memory requirements Read fasta files with sequences: Loading Loading
page2.Rmd +6 −5 Original line number Diff line number Diff line Loading @@ -2,15 +2,16 @@ title: Profile-HMM of coronavirus sequence --- # Solution using hmmer # Expects you have obtained data (explained on page1), expects aligned sequences ```bash apt get hmmer pip3 install pyfasta pyfasta split --header "fff/%(seqid)s.fasta" all.fasta hmmbuild MN908947.hmm MN908947.fasta hmmbuild output.hmm input_sequence.fasta ``` #(repeat for each sequence all call for all files in directory using bash command) # Another possible solution # Another possible solution in r # large memory requirements Read fasta files with sequences: Loading
