From d7b70467e118f77e47bd5a44566edf87d373f334 Mon Sep 17 00:00:00 2001 From: Helen Date: Mon, 26 Nov 2018 11:14:44 -0500 Subject: [PATCH 1/3] Code for questions 1 --- exercise1.sh | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 exercise1.sh diff --git a/exercise1.sh b/exercise1.sh new file mode 100644 index 0000000..be4e40c --- /dev/null +++ b/exercise1.sh @@ -0,0 +1,7 @@ +#To create file to align sporecoat files, first create sporecoatcombined.fasta by doing cat sporecoat01.fasta sporecoat02.fasta sporecoat03.fasta sporecoat04.fasta > sporecoatcombined.fasta and edit it so no sequence line containes > +#To create spore coat alignment +/afs/nd.edu/user5/hstreff/local/bin/muscle3.8.31_i86linux64 -in sporecoatcombined.fasta -out sporecoatalignment.align +#To create file to align transporter files, first create transportercombined.fasta by doing cat transporter01.fasta transporter02.fasta transporter03.fasta transporter04.fasta > transportercombined.fasta +#To create transporter alignment +/afs/nd.edu/user5/hstreff/local/bin/muscle3.8.31_i86linux64 -in transportercombined.fasta -out transporteralignment.align + From 4ad17d6b9fac56e92c6129fdcc849040b6197af6 Mon Sep 17 00:00:00 2001 From: Helen Date: Mon, 26 Nov 2018 11:16:07 -0500 Subject: [PATCH 2/3] Code for question 2 --- exercise2.sh | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 exercise2.sh diff --git a/exercise2.sh b/exercise2.sh new file mode 100644 index 0000000..6e6833c --- /dev/null +++ b/exercise2.sh @@ -0,0 +1,35 @@ +#To run use bash exercise2.sh +#Make transporteralignment.align into transporteralignment.hmm +/afs/nd.edu/user5/hstreff/local/bin/hmmbuiansporteralignment.hmm transporteralignment.align +#Determine number of hits with Arthrobacter +echo "transporterArthrobacter.hits" > transporterhits.txt +/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterArthrobacter.hits transporteralignment.hmm Arthrobacter.fasta +cat transporterArthrobacter.hits | grep -v "#" | wc -l >> transporterhits.txt +#Determine number of hits with Bacillus +echo "transporterBacillus.hits" >> transporterhits.txt +/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterBacillus.hits transporteralignment.hmm Bacillus.fasta +cat transporterBacillus.hits | grep -v "#" | wc -l >> transporterhits.txt +#Determine number of hits with Clostridium +echo "transporterClostridium.hits" >> transporterhits.txt +/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterClostridium.hits transporteralignment.hmm Clostridium.fasta +cat transporterClostridium.hits | grep -v "#" | wc -l >> transporterhits.txt +#Determine number of hits with Flavobacterium +echo "transporterFlavobacterium.hits" >> transporterhits.txt +/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterFlavobacterium.hits transporteralignment.hmm Flavobacterium.fasta +cat transporterFlavobacterium.hits | grep -v "#" | wc -l >> transporterhits.txt +#Determine number of hits with Limnohabitans +echo "transporterLimnohabitans.hits" >> transporterhits.txt +/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterLimnohabitans.hits transporteralignment.hmm Limnohabitans.fasta +cat transporterLimnohabitans.hits | grep -v "#" | wc -l >> transporterhits.txt +#Determine number of hits with Rhizobium +echo "transporterRhizobium.hits" >> transporterhits.txt +/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterRhizobium.hits transporteralignment.hmm Rhizobium.fasta +cat transporterRhizobium.hits | grep -v "#" | wc -l >> transporterhits.txt +#Determine number of hits with Roseobacter +echo "transporterRoseobacter.hits" >> transporterhits.txt +/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterRoseobacter.hits transporteralignment.hmm Roseobacter.fasta +cat transporterRoseobacter.hits | grep -v "#" | wc -l >> transporterhits.txt +#Determine number of hits with Verrucomicrobia +echo "transporterVerrucomicrobia.hits" >> transporterhits.txt +/afs/nd.edu/user5/hstreff/local/bin/hmmsearch --tblout transporterVerrucomicrobia.hits transporteralignment.hmm Verrucomicrobia.fasta +cat transporterVerrucomicrobia.hits | grep -v "#" | wc -l >> transporterhits.txt From be9df9bc05c525467f001e79fc8bb1c680b7c2e8 Mon Sep 17 00:00:00 2001 From: Helen Date: Mon, 26 Nov 2018 11:16:56 -0500 Subject: [PATCH 3/3] Hits for question 2 --- transporterhits.txt | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 transporterhits.txt diff --git a/transporterhits.txt b/transporterhits.txt new file mode 100644 index 0000000..d93ee9c --- /dev/null +++ b/transporterhits.txt @@ -0,0 +1,16 @@ +transporterArthrobacter.hits +0 +transporterBacillus.hits +1 +transporterClostridium.hits +0 +transporterFlavobacterium.hits +1 +transporterLimnohabitans.hits +1 +transporterRhizobium.hits +0 +transporterRoseobacter.hits +1 +transporterVerrucomicrobia.hits +0