Patrick O'Neil Submission

gene_sequences/script-problem1.sh

@@ -0,0 +1,23 @@
+#usage: bash script-problem1.sh
+#origin directory /afs/nd.edu/user30/poneil1/local/bin/IBC_EX11/gene_sequences
+
+#run each transporter file into an aligned sequence of their own and...
+#...combine these sequences into a single fasta file
+for transporter in transporter*.fasta
+do
+  	../../muscle -in $transporter -out transporterout.fasta
+        cat transporterout.fasta >> transporter-combined.fasta
+done
+#run the combined fasta file through muscle to align for final sequence
+../../muscle -in transporter-combined.fasta -out transporter-final.fasta
+
+#run each sporecoat file into an aligned sequence of their own and...
+#...combine these sequences into a single fasta file
+for sporecoat in sporecoat*
+do
+  	../../muscle -in $sporecoat -out sporecoatout.fasta
+        cat sporecoatout.fasta >> sporecoat-combined.fasta
+done
+
+#run the combined fasta file through muscle to align for final sequence
+../../muscle -in sporecoat-combined.fasta -out sporecoat-final.fasta

gene_sequences/script-problem2.sh

@@ -0,0 +1,14 @@
+#Usage: bash script-problem2.sh
+#HMMer searches each transporter fasta with each proteome fasta
+#initial working directory: gene_sequences
+for transporter in transporter0*.fasta
+        do
+          	for proteome in ../proteomes/*
+                        do
+                          	echo $transporter >> sequence-hits.txt
+                                echo $proteome >> sequence-hits.txt
+                                ../../hmmbuild transporter.hmm $transporter
+                                ../../hmmsearch transporter.hmm $proteome | grep$
+                        done
+        done
+

gene_sequences/sequence-hits.txt

@@ -0,0 +1,352 @@
+transporter01.fasta
+../proteomes/Arthrobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter01.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter01.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter01.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter01.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter01.fasta
+../proteomes/Roseobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter02.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter02.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter02.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter02.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter02.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter02.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter03.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter03.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter03.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter03.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter03.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter03.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter04.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Bacillus.fasta
+1 
+transporter04.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter04.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporter04.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter04.fasta
+../proteomes/Rhizobium.fasta
+2 
+transporter04.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter01.fasta
+../proteomes/Arthrobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter01.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter01.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter01.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter01.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter01.fasta
+../proteomes/Roseobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter02.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter02.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter02.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter02.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter02.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter02.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter03.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter03.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter03.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter03.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter03.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter03.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter04.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Bacillus.fasta
+1 
+transporter04.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter04.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporter04.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter04.fasta
+../proteomes/Rhizobium.fasta
+2 
+transporter04.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter-combined.fasta
+../proteomes/Arthrobacter.fasta
+transporter-combined.fasta
+../proteomes/Bacillus.fasta
+transporter-combined.fasta
+../proteomes/Clostridium.fasta
+transporter-combined.fasta
+../proteomes/Flavobacterium.fasta
+transporter-combined.fasta
+../proteomes/Limnohabitans.fasta
+transporter-combined.fasta
+../proteomes/Rhizobium.fasta
+transporter-combined.fasta
+../proteomes/Roseobacter.fasta
+transporter-combined.fasta
+../proteomes/Verrucomicrobia.fasta
+transporter-final.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter-final.fasta
+../proteomes/Bacillus.fasta
+1 
+transporter-final.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter-final.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporter-final.fasta
+../proteomes/Limnohabitans.fasta
+1 
+transporter-final.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter-final.fasta
+../proteomes/Roseobacter.fasta
+1 
+transporter-final.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporterout.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporterout.fasta
+../proteomes/Bacillus.fasta
+1 
+transporterout.fasta
+../proteomes/Clostridium.fasta
+0 
+transporterout.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporterout.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporterout.fasta
+../proteomes/Rhizobium.fasta
+2 
+transporterout.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporterout.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter01.fasta
+../proteomes/Arthrobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter01.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter01.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter01.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter01.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter01.fasta
+../proteomes/Roseobacter.fasta
+1 
+transporter01.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter02.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter02.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter02.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter02.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter02.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter02.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter02.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter03.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Bacillus.fasta
+0 
+transporter03.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter03.fasta
+../proteomes/Flavobacterium.fasta
+0 
+transporter03.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter03.fasta
+../proteomes/Rhizobium.fasta
+0 
+transporter03.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter03.fasta
+../proteomes/Verrucomicrobia.fasta
+0 
+transporter04.fasta
+../proteomes/Arthrobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Bacillus.fasta
+1 
+transporter04.fasta
+../proteomes/Clostridium.fasta
+0 
+transporter04.fasta
+../proteomes/Flavobacterium.fasta
+1 
+transporter04.fasta
+../proteomes/Limnohabitans.fasta
+0 
+transporter04.fasta
+../proteomes/Rhizobium.fasta
+2 
+transporter04.fasta
+../proteomes/Roseobacter.fasta
+0 
+transporter04.fasta
+../proteomes/Verrucomicrobia.fasta
+0