From 620b59018e1c5b6f92611b5df218377e357255cb Mon Sep 17 00:00:00 2001 From: Henry Perillo Date: Tue, 27 Nov 2018 19:24:21 -0500 Subject: [PATCH 1/3] Answer to first question of ex11 --- Exercise11part1.sh | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 Exercise11part1.sh diff --git a/Exercise11part1.sh b/Exercise11part1.sh new file mode 100644 index 0000000..fcf9971 --- /dev/null +++ b/Exercise11part1.sh @@ -0,0 +1,22 @@ +#First, move all sporecoat fasta files from laptop to remote computer using scp. + +#Then, cat all sporecoat fasta files into a single file +cat sporecoat01.fasta sporecoat02.fasta sporecoat03.fasta sporecoat04.fasta > sporecoatmerged.fasta + +#Remove '>' using sed and then manually add the first one back in using nano +sed 's/>//g' sporecoatmerged.fasta > sporecoatalignment.fasta + +#Next, run muscle command to generate align file and get alignment +muscle3.8.31_i86linux64 -in sporecoatalignment.fasta -out sporecoataligned.align + +#The next part is quite similar, as we move all transporter files to remote computer using scp + +#Then create final fasta file +cat transporter01.fasta transporter02.fasta transporter03.fasta transporter04.fasta > transportermerged.fasta + +#Remove all '>' and then manually add one to the first line using nano +sed 's/>//g' transportermerged.fasta > transporterfinal.fasta + +#Lastly, use muscle +muscle3.8.31_i86linux64 -in transporterfinal.fasta -out transporteraligned.align + From 8b8f7da10efa6acd3cf985064acceed631976b6f Mon Sep 17 00:00:00 2001 From: Henry Perillo Date: Tue, 27 Nov 2018 19:55:22 -0500 Subject: [PATCH 2/3] Exercise 11 part 2 answers --- Exercise11part2.sh | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 Exercise11part2.sh diff --git a/Exercise11part2.sh b/Exercise11part2.sh new file mode 100644 index 0000000..33246f2 --- /dev/null +++ b/Exercise11part2.sh @@ -0,0 +1,27 @@ +#Build HMM profile for transporter genes using transporterfinal.align +hmmbuild transporterfinal.hmm transporteraligned.align + +#Search in HMM for each species +hmmsearch --tblout transArthrobacter.hits transporterfinal.hmm Arthrobacter.fasta +cat transArthrobacter.hits | grep -v "#" | wc -l > transBachits.txt + +hmmsearch --tblout transBacillus.hits transporterfinal.hmm Bacillus.fasta +cat transBacillus.hits | grep -v "#" | wc -l >> transBachits.txt + +hmmsearch --tblout transClostridium.hits transporterfinal.hmm Clostridium.fasta +cat transClostridium.hits | grep -v "#" | wc -l >> transBachits.txt + +hmmsearch --tblout transFlavobacterium.hits transporterfinal.hmm Flavobacterium.fasta +cat transFlavobacterium.hits | grep -v "#" | wc -l >> transBachits.txt + +hmmsearch --tblout transLimnohabitans.hits transporterfinal.hmm Limnohabitans.fasta +cat transLimnohabitans.hits | grep -v "#" | wc -l >> transBachits.txt + +hmmsearch --tblout transRhizobium.hits transporterfinal.hmm Rhizobium.fasta +cat transRhizobium.hits | grep -v "#" | wc -l >> transBachits.txt + +hmmsearch --tblout transRoseobacter.hits transporterfinal.hmm Roseobacter.fasta +cat transRoseobacter.hits | grep -v "#" | wc -l >> transBachits.txt + +hmmsearch --tblout transVerrucomicrobia.hits transporterfinal.hmm Verrucomicrobia.fasta +cat transVerrucomicrobia.hits | grep -v "#" | wc -l >> transBachits.txt From 6255b204f80d820c470bc85eefed0535508e94aa Mon Sep 17 00:00:00 2001 From: Henry Perillo Date: Tue, 27 Nov 2018 19:58:55 -0500 Subject: [PATCH 3/3] Hits from part 2 --- Exercise11part2hits.sh | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 Exercise11part2hits.sh diff --git a/Exercise11part2hits.sh b/Exercise11part2hits.sh new file mode 100644 index 0000000..ae03c9f --- /dev/null +++ b/Exercise11part2hits.sh @@ -0,0 +1,11 @@ +#Concatenate file transBachits.txt to see the outputs +cat transBachits.txt +0 +1 +0 +0 +0 +0 +0 +0 +