Tatarian

unix-code-hmm.txt

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+#This is my shell script:
+
+#generate HMM profile for transporter gene
+
+../local/bin/hmmbuild transportergene.hmm ../transporterfiles.fasta.align
+
+#use hmm to search the 8 bacteria - record name and number of hits
+#Usage from proteomes folder: bash unix-code-hmm.txt
+
+for files in *.fasta
+
+do
+
+../local/bin/hmmsearch --tblout genehits.txt transportergene.hmm $files
+x=$(cat genehits.txt | grep -v "#" | wc -l)
+echo $files,$x >> finalgenehits.txt
+
+done
+
+#These are the results for the eight bacteria found in the finalgenehits.txt file:
+
+#Arthrobacter.fasta,0
+#Bacillus.fasta,1
+#Clostridium.fasta,0
+#Flavobacterium.fasta,1
+#Limnohabitans.fasta,1
+#Rhizobium.fasta,0
+#Roseobacter.fasta,1
+#Verrucomicrobia.fasta,0
+

unix-code-sequences.txt

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+#I condensed the four files for sporecoat and transporter, respectively, into single files in order to make the sequencing more efficient. See code below.
+
+cat sporecoat01.fasta sporecoat02.fasta sporecoat03.fasta sporecoat04.fasta > sporecoatfiles.fasta
+cat transporter01.fasta transporter02.fasta transporter03.fasta transporter04.fasta > transporterfiles.fasta
+
+#I had to manually enter a few line breaks where necessary in order for the sequencing to run smoothly.
+
+#I then copied them into the remote computer file in order to use the muscle tool, using the code below.
+
+scp sporecoatfiles.fasta [email protected]:/afs/nd.edu/user35
+scp transporterfiles.fasta [email protected]:/afs/nd.edu/user35/atataria
+
+#Once the files where in the remote drive, I ran muscle to get the sequence alignments as shown below.
+
+[atataria@remote107 ~]$ muscle3.8.31_i86linux64 -in sporecoatfiles.fasta -out sporecoatfiles.fasta.align
+
+MUSCLE v3.8.31 by Robert C. Edgar
+
+http://www.drive5.com/muscle
+This software is donated to the public domain.
+Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
+
+sporecoatfiles 26 seqs, max length 152, avg  length 138
+00:00:00     10 MB(1%)  Iter   1  100.00%  K-mer dist pass 1
+00:00:00     10 MB(1%)  Iter   1  100.00%  K-mer dist pass 2
+00:00:00     14 MB(1%)  Iter   1  100.00%  Align node       
+00:00:00     14 MB(1%)  Iter   1  100.00%  Root alignment
+00:00:00     14 MB(1%)  Iter   2  100.00%  Refine tree   
+00:00:00     14 MB(1%)  Iter   2  100.00%  Root alignment
+00:00:00     14 MB(1%)  Iter   2  100.00%  Root alignment
+00:00:00     14 MB(1%)  Iter   3  100.00%  Refine biparts
+00:00:00     14 MB(1%)  Iter   4  100.00%  Refine biparts
+00:00:00     14 MB(1%)  Iter   5  100.00%  Refine biparts
+00:00:00     14 MB(1%)  Iter   6  100.00%  Refine biparts
+00:00:00     14 MB(1%)  Iter   7  100.00%  Refine biparts
+00:00:00     14 MB(1%)  Iter   8  100.00%  Refine biparts
+00:00:00     14 MB(1%)  Iter   9  100.00%  Refine biparts
+00:00:01     14 MB(1%)  Iter  10  100.00%  Refine biparts
+[atataria@remote107 ~]$ muscle3.8.31_i86linux64 -in transporterfiles.fasta -out transporterfiles.fasta.align
+
+MUSCLE v3.8.31 by Robert C. Edgar
+
+http://www.drive5.com/muscle
+This software is donated to the public domain.
+Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
+
+transporterfiles 4 seqs, max length 412, avg  length 410
+00:00:00     10 MB(1%)  Iter   1  100.00%  K-mer dist pass 1
+00:00:00     10 MB(1%)  Iter   1  100.00%  K-mer dist pass 2
+00:00:00     13 MB(1%)  Iter   1  100.00%  Align node       
+00:00:00     13 MB(1%)  Iter   1  100.00%  Root alignment
+00:00:00     13 MB(1%)  Iter   2  100.00%  Root alignment
+00:00:00     13 MB(1%)  Iter   3  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter   4  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter   5  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter   6  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter   7  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter   8  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter   9  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter  10  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter  11  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter  12  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter  13  100.00%  Refine biparts
+00:00:00     13 MB(1%)  Iter  14  100.00%  Refine biparts