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Gretchen Andreasen, Carol de Souza Moreira, Isabella Gimon #6

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6955f7f
Final gene count script file and suggested proteomes script file and …
Oct 13, 2022
c7a1d02
Added an E-value threshold of 0.1, per the suggestion of a research f…
Oct 14, 2022
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3 changes: 3 additions & 0 deletions bash_group_members.txt
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Gretchen Andreasen
Carol de Souza Moreira
Isabella Gimon
50 changes: 50 additions & 0 deletions file_list
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proteome_01
proteome_02
proteome_03
proteome_04
proteome_05
proteome_06
proteome_07
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proteome_09
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proteome_11
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57 changes: 57 additions & 0 deletions gene_count.sh
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#!/bin/bash
# Usage: bash gene_count.sh "gene1" "gene2"
# This script counts all of the occurrences of gene 1 and gene 2 in proteome files. Gene names are case-sensitive.
# This script works under the assumption that the user's file paths are as such:
# pwd is the current project file, containing folders with the proteome sequences and reference sequences for both genes.
# ./proteomes
# ./ref_sequences
# all tools needed (muscle, hmmsearch, and hmmbuild) are located in an accessible tools folder outside of the project file
# ../tools
# Created by: Gretchen Andreasen, Carol de Souza Moreira, Isabella Gimon

# To start, we need to concatenate all of the reference sequences into one file per type (one file for gene 1, one file for gene 2)
cat ref_sequences/$1* >> ref_sequences/$1_all
cat ref_sequences/$2* >> ref_sequences/$2_all

@qtran4 qtran4 Oct 21, 2022

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+2

# Next let's align these reference genes
../tools/muscle -in ref_sequences/$1_all -out ref_sequences/$1_aligned
../tools/muscle -in ref_sequences/$2_all -out ref_sequences/$2_aligned

@qtran4 qtran4 Oct 21, 2022

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+3

# Now let's use hmmbuild and build a profile (to use hmmsearch with)
../tools/hmmbuild ref_sequences/$1_profile ref_sequences/$1_aligned
../tools/hmmbuild ref_sequences/$2_profile ref_sequences/$2_aligned

@qtran4 qtran4 Oct 21, 2022

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+3

# Now let's use hmmsearch to search for gene 1 and gene 2 in the proteomes
# To do this easily, make a list of all the files you want searched
ls proteomes | sed 's/.fasta//g' > file_list
# We also need specific directories for gene 1 and gene 2 results
mkdir $1_results
mkdir $2_results

# Now let's count gene 1; there is an e-value filter placed on this search (and the next) to minimize the amount gene assignments through random chance. The E-value of 0.1 is used per the suggestions of this research forum post <https://www.researchgate.net/post/What-e-value-do-you-use-as-a-cutoff-and-for-what-purpose-when-you-are-computing-a-BLAST>.
for i in `cat file_list`
do
../tools/hmmsearch -E "0.1" --tblout $1_results/$i ref_sequences/$1_profile proteomes/$i.fasta
done

# And gene 2; the same E-value filter as before.
for i in `cat file_list`
do
../tools/hmmsearch -E "0.1" --tblout $2_results/$i ref_sequences/$2_profile proteomes/$i.fasta
done

@qtran4 qtran4 Oct 21, 2022

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+2

# Now to present the data. First we need to count the search results
# Count the number of mcra genes in the proteome search results
for i in `cat file_list`
do
cat $1_results/$i | grep -E -o "$1_aligned" | wc -l
done > proteome_$1_results

# Count the number of hsp70 genes in the proteome search results
for i in `cat file_list`
do
cat $2_results/$i | grep -E -o "$2_aligned" | wc -l
done > proteome_$2_results

# Combine the list of files and corresponding search results, and write a header for the data
{ echo -e "proteome $1_count $2_count"; paste file_list proteome_$1_results proteome_$2_results | column -s $'\t' -t; } > proteome_final.txt

@qtran4 qtran4 Oct 21, 2022

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+4

@qtran4 qtran4 Oct 21, 2022

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-header comments, including usage line [1 point]
-general commenting of code throughout script [1 point]
-code efficiency [2 points]

17 changes: 17 additions & 0 deletions hsp70_results/proteome_01
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_013362005.1 - hsp70_aligned - 7.3e-297 982.9 30.6 8.2e-297 982.7 30.6 1.0 1 0 0 1 1 1 1 molecular chaperone DnaK
WP_013360607.1 - hsp70_aligned - 4.4e-129 428.7 0.2 6.4e-129 428.1 0.2 1.1 1 0 0 1 1 1 1 molecular chaperone HscC
WP_013362571.1 - hsp70_aligned - 4.4e-12 42.2 6.4 1.9e-11 40.1 6.4 2.1 1 1 0 1 1 1 1 rod shape-determining protein
WP_013360481.1 - hsp70_aligned - 1.2e-08 30.9 2.3 0.00025 16.6 0.5 2.7 2 1 0 3 3 3 2 ethanolamine utilization protein EutJ
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_01.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_01 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_01.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:09 2022
# [ok]
15 changes: 15 additions & 0 deletions hsp70_results/proteome_02
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_010867429.1 - hsp70_aligned - 0.0067 11.4 6.5 0.0083 11.2 6.5 1.1 1 0 0 1 1 1 1 transcriptional regulator
WP_010868356.1 - hsp70_aligned - 0.014 10.4 3.6 0.015 10.3 3.6 1.1 1 0 0 1 1 1 0 hypothetical protein
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_02.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_02 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_02.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:09 2022
# [ok]
16 changes: 16 additions & 0 deletions hsp70_results/proteome_03
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_048118742.1 - hsp70_aligned - 0 1101.3 23.8 0 1101.1 23.8 1.0 1 0 0 1 1 1 1 MULTISPECIES: molecular chaperone DnaK
WP_048116754.1 - hsp70_aligned - 6.5e-110 365.8 8.9 2.2e-100 334.3 3.6 2.0 2 0 0 2 2 2 2 MULTISPECIES: hypothetical protein
WP_048116752.1 - hsp70_aligned - 6.8e-107 355.8 13.6 8.6e-100 332.4 6.5 2.0 2 0 0 2 2 2 2 MULTISPECIES: Hsp70 family protein
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_03.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_03 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_03.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:09 2022
# [ok]
17 changes: 17 additions & 0 deletions hsp70_results/proteome_04
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_055360419.1 - hsp70_aligned - 3.6e-262 868.4 31.3 9.8e-233 771.2 25.6 2.0 1 1 1 2 2 2 2 molecular chaperone DnaK
WP_055360541.1 - hsp70_aligned - 1.1e-156 520.0 14.1 1.1e-143 477.1 12.9 2.0 2 0 0 2 2 2 2 Fe-S protein assembly chaperone HscA
WP_055359523.1 - hsp70_aligned - 2.5e-14 49.8 0.3 1.5e-13 47.2 0.0 2.2 3 0 0 3 3 3 1 MULTISPECIES: rod shape-determining protein
WP_055361642.1 - hsp70_aligned - 7.3e-06 21.8 3.4 0.01 11.5 0.1 3.1 3 1 1 4 4 4 2 cell division protein FtsA
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_04.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_04 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_04.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:09 2022
# [ok]
15 changes: 15 additions & 0 deletions hsp70_results/proteome_05
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_011447201.1 - hsp70_aligned - 9.2e-302 999.4 26.8 1e-301 999.3 26.8 1.0 1 0 0 1 1 1 1 molecular chaperone DnaK
WP_052288776.1 - hsp70_aligned - 2.8e-147 489.1 3.1 4e-147 488.7 2.8 1.2 1 1 0 1 1 1 1 hypothetical protein
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_05.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_05 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_05.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:10 2022
# [ok]
13 changes: 13 additions & 0 deletions hsp70_results/proteome_06
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_06.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_06 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_06.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:10 2022
# [ok]
15 changes: 15 additions & 0 deletions hsp70_results/proteome_07
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_012106756.1 - hsp70_aligned - 7.1e-294 973.0 23.7 8.1e-294 972.8 23.7 1.0 1 0 0 1 1 1 1 molecular chaperone DnaK
WP_012107167.1 - hsp70_aligned - 2.5e-292 967.9 18.7 2.9e-292 967.7 18.7 1.0 1 0 0 1 1 1 1 molecular chaperone DnaK
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_07.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_07 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_07.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:10 2022
# [ok]
18 changes: 18 additions & 0 deletions hsp70_results/proteome_08
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_062403955.1 - hsp70_aligned - 1.2e-259 860.3 33.0 4.2e-230 762.7 27.0 2.0 1 1 1 2 2 2 2 molecular chaperone DnaK
WP_062405703.1 - hsp70_aligned - 7.3e-153 507.6 11.9 1.1e-151 503.7 11.9 1.9 1 1 0 1 1 1 1 Fe-S protein assembly chaperone HscA
WP_062406926.1 - hsp70_aligned - 5.4e-24 81.9 0.0 5.5e-19 65.3 0.0 2.0 2 0 0 2 2 2 2 Hsp70 family protein
WP_062408136.1 - hsp70_aligned - 1.1e-13 47.8 0.5 6.3e-13 45.3 0.0 2.2 3 0 0 3 3 3 1 rod shape-determining protein
WP_062406075.1 - hsp70_aligned - 1.6e-06 24.2 2.1 0.0025 13.6 0.1 3.1 3 1 1 4 4 4 2 cell division protein FtsA
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_08.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_08 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_08.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:10 2022
# [ok]
14 changes: 14 additions & 0 deletions hsp70_results/proteome_09
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_010902322.1 - hsp70_aligned - 0 1049.3 32.0 0 1049.1 32.0 1.0 1 0 0 1 1 1 1 molecular chaperone DnaK
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_09.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_09 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_09.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:10 2022
# [ok]
16 changes: 16 additions & 0 deletions hsp70_results/proteome_10
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_010937085.1 - hsp70_aligned - 1.3e-280 928.4 26.7 6.4e-251 830.3 19.6 2.0 1 1 1 2 2 2 2 molecular chaperone DnaK
WP_010936122.1 - hsp70_aligned - 0.00098 13.8 0.1 0.0015 13.2 0.1 1.4 1 0 0 1 1 1 1 cell division protein FtsA
WP_010936412.1 - hsp70_aligned - 0.0011 13.6 0.1 0.002 12.8 0.1 1.3 1 0 0 1 1 1 1 cell division protein FtsA
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_10.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_10 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_10.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:10 2022
# [ok]
19 changes: 19 additions & 0 deletions hsp70_results/proteome_11
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
WP_015941672.1 - hsp70_aligned - 1.5e-282 936.2 18.1 1.5e-280 929.5 18.1 2.0 1 1 0 1 1 1 1 molecular chaperone DnaK
WP_015941419.1 - hsp70_aligned - 1.8e-278 922.7 13.0 1.7e-246 817.1 7.3 2.0 1 1 1 2 2 2 2 molecular chaperone DnaK
WP_015942306.1 - hsp70_aligned - 1.3e-34 117.2 0.0 1.2e-19 67.8 0.0 3.0 2 1 1 3 3 3 3 Hsp70 family protein
WP_012616464.1 - hsp70_aligned - 1e-11 41.6 6.1 2e-11 40.6 6.1 1.6 1 1 0 1 1 1 1 rod shape-determining protein
WP_012616267.1 - hsp70_aligned - 3.6e-11 39.8 5.1 1.1e-09 34.9 5.1 2.6 1 1 0 1 1 1 1 rod shape-determining protein
WP_015941576.1 - hsp70_aligned - 5.1e-05 19.4 0.9 0.00028 17.0 0.1 2.2 2 0 0 2 2 2 1 cell division protein FtsA
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: ref_sequences/hsp70_profile
# Target file: proteomes/proteome_11.fasta
# Option settings: ../tools/hmmsearch --tblout hsp70_results/proteome_11 -E 0.1 ref_sequences/hsp70_profile proteomes/proteome_11.fasta
# Current dir: /afs/crc.nd.edu/user/m/mandrea1/Private/Intro_Biocomputing_BIOS_60318/bash_project
# Date: Thu Oct 13 21:29:10 2022
# [ok]
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