From 1d0c70f6ca56a325fe4663ea2cc85fa3fddd7942 Mon Sep 17 00:00:00 2001 From: Alexis Magana Date: Wed, 28 Nov 2018 00:49:28 -0500 Subject: [PATCH 1/2] Added file for problem 1 --- EX11Problem1.sh | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 EX11Problem1.sh diff --git a/EX11Problem1.sh b/EX11Problem1.sh new file mode 100644 index 0000000..d32a910 --- /dev/null +++ b/EX11Problem1.sh @@ -0,0 +1,14 @@ +for file in IBC_EX11/gene_sequences/s* +do + cat $file>> sporecoatTot.fasta #Cats the files for sporecoat + echo \n >> sporecoatTot.fasta #Adds the newline to the end +done +for file in IBC_EX11/gene_sequences/t* +do + cat $file>> transporterTot.fasta #Cats the files for transporter + echo \n >> transporterTot.fasta #Adds the new line to the end +done + +./muscle3.8.31_i86linux64 -in sporecoatTot.fasta -out sporecoatTot.align #creates align for sporecoat +./muscle3.8.31_i86linux64 -in transporterTot.fasta -out transporterTot.align #Creates align for transporter + From c0ea370fee72bd59d913ab83a7b468315cfebbe1 Mon Sep 17 00:00:00 2001 From: Alexis Magana Date: Wed, 28 Nov 2018 00:50:15 -0500 Subject: [PATCH 2/2] Added file for problem 2 --- EX11_Problem2.sh | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 EX11_Problem2.sh diff --git a/EX11_Problem2.sh b/EX11_Problem2.sh new file mode 100644 index 0000000..1da73d5 --- /dev/null +++ b/EX11_Problem2.sh @@ -0,0 +1,7 @@ +./local/bin/hmmbuild transporterTot.hmm transporterTot.align #creates the hmm file +for file in IBC_EX11/proteomes/*.fasta #for all the files in proteomes +do +./local/bin/hmmsearch --tblout $file.hits transporterTot.hmm $file #creates a hit file with matches +echo "Number of hits in $(echo "$file") is $(cat $file.hits| grep -v "#"| wc -l)">>Hits_In_File.txt #tells the file and number of hits +done +