timaburton · hlaboe · Oct 14, 2021
diff --git a/bioinformaticsProject/BioinformaticsProject.sh b/bioinformaticsProject/BioinformaticsProject.sh
@@ -0,0 +1,38 @@
+#Searches set of proteomes for the mcrA and hsp70 genes, and outputs results into a table, in a file titled "Summary.csv". Produces a file "Candidates.txt" that contains a list of proteomes that are candidates for the growth experiments.
+#Note: The code is dependent on where tools and files are located in a system, so could vary for users. 
+#Usage: bash BioinformaticsProject.sh
+
+#Align reference sequences
+cd ref_sequences
+cat mcrAgene_**.fasta > mcrAgene.fasta
+cat hsp70gene_**.fasta > hsp70gene.fasta
+../muscle -in mcrAgene.fasta -out mcrAgene_muscle.fasta
+../muscle -in hsp70gene.fasta -out hsp70gene_muscle.fasta
+
+#Build a profile for the mcrA and hsp70 genes
+../bin/hmmbuild --amino mcrAgene_hmm.txt mcrAgene_muscle.fasta
+../bin/hmmbuild --amino hsp70gene_hmm.txt hsp70gene_muscle.fasta
+
+#Search the proteomes for mcrA gene, identifies methanogens
+cd ../proteomes
+for number in proteome_**.fasta
+do
+name=$(echo $number | cut -d_ -f 2 | cut -d. -f 1)
+../bin/hmmsearch --tblout ${name}resultsmcrAgene_match ../ref_sequences/mcrAgene_hmm.txt $number
+../bin/hmmsearch --tblout ${name}resultshsp70gene_match ../ref_sequences/hsp70gene_hmm.txt $number
+done
+
+#Produce a table with proteome number, mcrA match, number of hsp70 matches
+for n in {01..50}
+do
+column2=$(cat "$n"resultsmcrAgene_match | grep -v '#' | wc -l)
+column3=$(cat "$n"resultshsp70gene_match | grep -v '#' | wc -l)
+echo "Proteome $n" "$column2" "$column3" >> ../Summary.csv
+done
+
+#Provide a list of candidate pH-resistant methanogens
+#Based on the results, the cutoff for sufficient pH resistance was 1 copy of hsp70. While the average number of copies was 2.62 across the proteomes, only 14/50 were methanogens. Considering pH resistance to be just one copy of hsp70 allows you to proceed with a larger sample for the growht experiments.
+#Note: Average was calculated by awk '{ total += $3; count++ } END { print total/count }' Summary.csv
+cd ..
+grep -e '1 [1-9]' Summary.csv > Candidates.txt
+
diff --git a/bioinformaticsProject/Candidates.txt b/bioinformaticsProject/Candidates.txt
@@ -0,0 +1,13 @@
+Proteome 03 1 3
+Proteome 05 1 2
+Proteome 07 1 2
+Proteome 15 1 1
+Proteome 16 1 1
+Proteome 24 1 2
+Proteome 38 1 1
+Proteome 39 1 1
+Proteome 42 1 3
+Proteome 44 1 1
+Proteome 45 1 3
+Proteome 48 1 1
+Proteome 50 1 3
diff --git a/bioinformaticsProject/Summary.csv b/bioinformaticsProject/Summary.csv
@@ -0,0 +1,50 @@
+Proteome 01 0 4
+Proteome 02 0 2
+Proteome 03 1 3
+Proteome 04 0 4
+Proteome 05 1 2
+Proteome 06 0 0
+Proteome 07 1 2
+Proteome 08 0 5
+Proteome 09 0 1
+Proteome 10 0 3
+Proteome 11 0 6
+Proteome 12 0 6
+Proteome 13 0 3
+Proteome 14 0 2
+Proteome 15 1 1
+Proteome 16 1 1
+Proteome 17 0 4
+Proteome 18 0 8
+Proteome 19 2 1
+Proteome 20 0 3
+Proteome 21 0 5
+Proteome 22 0 9
+Proteome 23 2 2
+Proteome 24 1 2
+Proteome 25 0 5
+Proteome 26 0 1
+Proteome 27 0 1
+Proteome 28 0 1
+Proteome 29 1 0
+Proteome 30 0 1
+Proteome 31 0 7
+Proteome 32 0 4
+Proteome 33 0 0
+Proteome 34 0 2
+Proteome 35 0 1
+Proteome 36 0 3
+Proteome 37 0 1
+Proteome 38 1 1
+Proteome 39 1 1
+Proteome 40 0 2
+Proteome 41 0 1
+Proteome 42 1 3
+Proteome 43 0 3
+Proteome 44 1 1
+Proteome 45 1 3
+Proteome 46 0 2
+Proteome 47 0 1
+Proteome 48 1 1
+Proteome 49 0 3
+Proteome 50 1 3
diff --git a/bioinformaticsProject/bin/alimask b/bioinformaticsProject/bin/alimask
diff --git a/bioinformaticsProject/bin/hmmalign b/bioinformaticsProject/bin/hmmalign
diff --git a/bioinformaticsProject/bin/hmmbuild b/bioinformaticsProject/bin/hmmbuild
diff --git a/bioinformaticsProject/bin/hmmconvert b/bioinformaticsProject/bin/hmmconvert
diff --git a/bioinformaticsProject/bin/hmmemit b/bioinformaticsProject/bin/hmmemit
diff --git a/bioinformaticsProject/bin/hmmfetch b/bioinformaticsProject/bin/hmmfetch
diff --git a/bioinformaticsProject/bin/hmmlogo b/bioinformaticsProject/bin/hmmlogo
diff --git a/bioinformaticsProject/bin/hmmpgmd b/bioinformaticsProject/bin/hmmpgmd
diff --git a/bioinformaticsProject/bin/hmmpgmd_shard b/bioinformaticsProject/bin/hmmpgmd_shard
diff --git a/bioinformaticsProject/bin/hmmpress b/bioinformaticsProject/bin/hmmpress
diff --git a/bioinformaticsProject/bin/hmmscan b/bioinformaticsProject/bin/hmmscan
diff --git a/bioinformaticsProject/bin/hmmsearch b/bioinformaticsProject/bin/hmmsearch
diff --git a/bioinformaticsProject/bin/hmmsim b/bioinformaticsProject/bin/hmmsim
diff --git a/bioinformaticsProject/bin/hmmstat b/bioinformaticsProject/bin/hmmstat
diff --git a/bioinformaticsProject/bin/jackhmmer b/bioinformaticsProject/bin/jackhmmer
diff --git a/bioinformaticsProject/bin/makehmmerdb b/bioinformaticsProject/bin/makehmmerdb
diff --git a/bioinformaticsProject/bin/nhmmer b/bioinformaticsProject/bin/nhmmer
diff --git a/bioinformaticsProject/bin/nhmmscan b/bioinformaticsProject/bin/nhmmscan
diff --git a/bioinformaticsProject/bin/phmmer b/bioinformaticsProject/bin/phmmer
diff --git a/bioinformaticsProject/hmmer/.gitignore b/bioinformaticsProject/hmmer/.gitignore
@@ -0,0 +1,48 @@
+configure
+config.log
+config.status
+Makefile
+easel
+*.o
+*.dSYM
+*.stamp
+src/*_example
+src/*_example?
+src/*_utest
+src/*_benchmark
+src/*_stats
+src/impl
+src/impl*/*_example
+src/impl*/*_utest
+src/impl*/*_benchmark
+documentation/userguide/copyright.tex
+documentation/userguide/titlepage.tex
+documentation/man/*.man
+libdivsufsort/divsufsort.h
+libdivsufsort/libdivsufsort.a
+src/libhmmer.a
+src/p7_config.h
+profmark/create-profmark
+profmark/rocplot
+src/alimask
+src/hmmalign
+src/hmmbuild
+src/hmmc2
+src/hmmconvert
+src/hmmemit
+src/hmmerfm-exactmatch
+src/hmmfetch
+src/hmmlogo
+src/hmmpgmd
+src/hmmpgmd_shard
+src/hmmpress
+src/hmmscan
+src/hmmsearch
+src/hmmsim
+src/hmmstat
+src/itest_brute
+src/jackhmmer
+src/makehmmerdb
+src/nhmmer
+src/nhmmscan
+src/phmmer
diff --git a/bioinformaticsProject/hmmer/.travis.yml b/bioinformaticsProject/hmmer/.travis.yml
@@ -0,0 +1,14 @@
+language: c
+
+env:
+  - SQC_NONZERO_EXIT=1
+
+script:
+  - git clone -b develop https://github.com/${TRAVIS_REPO_SLUG/hmmer/easel}.git
+  - ln -s easel/aclocal.m4 aclocal.m4
+  - autoconf
+  - ./configure
+  - make
+  - make dev
+  - make check
+
diff --git a/bioinformaticsProject/hmmer/INSTALL b/bioinformaticsProject/hmmer/INSTALL
@@ -0,0 +1,20 @@
+Brief installation instructions 
+HMMER 3.3.2 (Nov 2020)
+
+Starting from a source distribution, hmmer-3.3.2.tar.gz:
+   uncompress hmmer-3.3.2.tar.gz  
+   tar xf hmmer-3.3.2.tar
+   cd hmmer-3.3.2
+   ./configure
+   make
+   make check                        # optional: automated tests
+   make install                      # optional: install HMMER programs and man pages
+   (cd easel; make install)          # optional: install Easel tools too
+
+For more details including customization, supported platforms, and
+troubleshooting, see the Installation chapter in the HMMER User's
+Guide (Userguide.pdf).
+
+
+
+
diff --git a/bioinformaticsProject/hmmer/LICENSE b/bioinformaticsProject/hmmer/LICENSE
@@ -0,0 +1,93 @@
+HMMER - Biological sequence analysis with profile hidden Markov models
+Copyright (C) 1992-2020 Sean R. Eddy
+Copyright (C) 2000-2020 Howard Hughes Medical Institute
+Copyright (C) 2015-2020 President and Fellows of Harvard College
+Copyright (C) 1992-2004 Washington University School of Medicine
+Copyright (C) 1992-1994 MRC Laboratory of Molecular Biology
+-----------------------------------------------------------------------
+
+The code includes contributions and input from current and past
+members of the HMMER development team, as well as other colleagues and
+sources, including:
+
+   Bill Arndt        
+   Jeremy Buhler     
+   Tyler Camp
+   Nick Carter        
+   Sergi Castellano  
+   Goran Ceric       
+   Michael Farrar    
+   Rob Finn          
+   Ian Holmes        
+   Bjarne Knudsen    
+   Diana Kolbe       
+   Erik Lindahl      
+   Graeme Mitchison  
+   Eric Nawrocki     
+   Lee Newberg       
+   Elena Rivas        
+   Walt Shands  
+   Travis Wheeler    
+
+HMMER also includes copyrighted and licensed code that has been
+incorporated from other sources, including:
+
+   Yuta Mori (libdivsufsort-lite)
+   Apple Computer                  
+   Free Software Foundation, Inc.  
+   IBM TJ Watson Research Center   
+   X Consortium                    
+
+HMMER uses the Easel software library, which has its own license and
+copyright information. See easel/LICENSE.
+
+HMMER includes patent-pending SIMD technology under a nonexclusive
+license from the estate of Michael Farrar. You are sublicensed to use
+this technology specifically for the use, modification, and
+redistribution of HMMER.
+
+HMMER development is supported in part by the National Human Genome
+Research Institute of the US National Institutes of Health under grant
+number R01HG009116. The content is solely the responsibility of the
+authors and does not necessarily represent the official views of the
+National Institutes of Health.
+
+HMMER source code is distributed as open source under the terms of the
+BSD three-clause license:
+
+   Redistribution and use in source and binary forms, with or without
+   modification, are permitted provided that the following conditions
+   are met:
+
+   1. Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above
+      copyright notice, this list of conditions and the following
+      disclaimer in the documentation and/or other materials provided
+      with the distribution.
+
+   3. Neither the name of any copyright holder nor the names of 
+      contributors may be used to endorse or promote products derived
+      from this software without specific prior written permission.
+
+   THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+   "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+   LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+   FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+   COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+   INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+   (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+   SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+   HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+   STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+   ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+   OF THE POSSIBILITY OF SUCH DAMAGE.
+
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