Wang_Serene_Exercise11_Submission

Exercise11.sh

@@ -0,0 +1,180 @@
+####QUESTION1####
+
+
+###Align reference sequence files using muscle either format below is okay! Repeat alignment for all files.
+
+#Sigma
+/Users/lou/Desktop/muscle3.8.31_i86darwin64 -in sigma.ref -out sigma.align
+
+#transporter reference
+/Users/lou/Desktop/muscle3.8.31_i86darwin64 -in transporter.ref -out transporter.align
+
+#sporecoat
+/Users/lou/Desktop/muscle3.8.31_i86darwin64 -in sporecoat.ref -out sporecoat.align
+
+
+###Build a profile HMM using alignment sequences and hmmbuild.
+
+#Sigma
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmbuild sigma.hmm sigma.align
+
+#transporter reference
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmbuild transporter.hmm transporter.align
+
+#sporecoat
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmbuild sporecoat.hmm sporecoat.align
+
+
+###Search each proteome for sigma factors using hmmsearch.
+
+#Arthrobacter
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sigma.hmm Arthrobacter.fasta
+cat Results.txt >> All_Sigma_Results.txt
+
+#Bacillus
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sigma.hmm Bacillus.fasta
+cat Results.txt >> All_Sigma_Results.txt
+
+#Clostridium
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout cat Results.txt sigma.hmm Clostridium.fasta
+cat Results.txt >> All_Sigma_Results.txt
+
+#Flavobacterium
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sigma.hmm Flavobacterium.fasta
+cat Results.txt >> All_Sigma_Results.txt
+
+#Limnohabitans
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sigma.hmm Limnohabitans.fasta
+cat Results.txt >> All_Sigma_Results.txt
+
+#Rhizobium
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sigma.hmm Rhizobium.fasta
+cat Results.txt >> All_Sigma_Results.txt
+
+#Roseobacter
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sigma.hmm Roseobacter.fasta
+cat Results.txt >> All_Sigma_Results.txt
+
+#Verrucomicrobia
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sigma.hmm Verrucomicrobia.fasta
+cat Results.txt >> All_Sigma_Results.txt
+
+
+###Search each proteome for transporter using hmmsearch.
+
+#Arthrobacter
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt transporter.hmm Arthrobacter.fasta
+cat Results.txt >> All_Transporter_Results.txt
+
+#Bacillus
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Bacillus.txt transporter.hmm Bacillus.fasta
+cat Results.txt >> All_Transporter_Results.txt
+
+#Clostridium
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt transporter.hmm Clostridium.fasta
+cat Results.txt >> All_Transporter_Results.txt
+
+#Flavobacterium
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt transporter.hmm Flavobacterium.fasta
+cat Results.txt >> All_Transporter_Results.txt
+
+#Limnohabitans
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Limnohabitans.txt transporter.hmm Limnohabitans.fasta
+cat Results.txt >> All_Transporter_Results.txt
+
+#Rhizobium
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt transporter.hmm Rhizobium.fasta
+cat Results.txt >> All_Transporter_Results.txt
+
+#Roseobacter
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt transporter.hmm Roseobacter.fasta
+cat Results.txt >> All_Transporter_Results.txt
+
+#Verrucomicrobia
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt transporter.hmm Verrucomicrobia.fasta
+cat Results.txt >> All_Transporter_Results.txt
+
+
+###Search each proteome for sporecoat using hmmsearch.
+
+#Arthrobacter
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sporecoat.hmm Arthrobacter.fasta
+cat Results.txt >> All_Sporecoat_Results.txt
+
+#Bacillus
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sporecoat.hmm Bacillus.fasta
+cat Results.txt >> All_Sporecoat_Results.txt
+
+#Clostridium
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sporecoat.hmm Clostridium.fasta
+cat Results.txt >> All_Sporecoat_Results.txt
+
+#Flavobacterium
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sporecoat.hmm Flavobacterium.fasta
+cat Results.txt >> All_Sporecoat_Results.txt
+
+#Limnohabitans
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sporecoat.hmm Limnohabitans.fasta
+cat Results.txt >> All_Sporecoat_Results.txt
+
+#Rhizobium
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sporecoat.hmm Rhizobium.fasta
+cat Results.txt >> All_Sporecoat_Results.txt
+
+#Roseobacter
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sporecoat.hmm Roseobacter.fasta
+cat Results.txt >> All_Sporecoat_Results.txt
+
+#Verrucomicrobia
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt sporecoat.hmm Verrucomicrobia.fasta
+cat Results.txt >> All_Sporecoat_Results.txt
+
+
+#Combine the three results files in one file called ALL_Results.txt
+cat All_Sigma_Results.txt >> ALL_Results.txt
+cat All_Transporter_Results.txt >> ALL_Results.txt
+cat All_Sporecoat_Results.txt >> ALL_Results.txt
+
+#Remove comments and put into a new file called ALL1.txt
+grep -v '[#]' ALL_Results.txt>ALL1.txt
+
+#Cut out rows 1, 3, and 5 and put into a new file called ALL2.txt
+awk '{print $1,$3,$5}' ALL1.txt > ALL2.txt 
+
+#Trim first colmun contents and put into new file called FinalResults.txt
+sed -E 's/tr\|[A-Z0-9]+\|[A-Z0-9]+_9//g' ALL2.txt >> FinalResults.txt
+
+
+
+
+## Problem 2
+
+# Set working Directory
+setwd("C:/Users/Michelle Wang/Desktop/BIOS 60318/Intro_Biocomp_ND_317_Tutorial11/Exercise11_files/Problem2/")
+
+# Load Libraries
+library(stringr)
+
+# Scan file into vector 
+data = scan(file = "motifsort.fasta",sep="\t", what = character())
+
+#  Search for sequence and write to new file
+for(i in 2:length(data)){
+  # Separate sequence ID
+  if (str_detect(data[i-1],">")=='TRUE'){
+    seq = data[i-1]
+    }
+  else if (str_detect(data[i],"(AKKPRVZE)")=='TRUE'){
+    write(seq, file = "motif1", append = TRUE)
+    write(data[i], file = "motif1", append = TRUE)
+  }
+  else if (str_detect(data[i],"(AAQWWRNYGG)")=='TRUE'){
+    write(seq, file = "motif2", append = TRUE)
+    write(data[i], file = "motif2", append = TRUE)
+  }
+  else {
+    write(seq, file = "other", append = TRUE)
+    write(data[i], file = "other", append = TRUE)
+  }
+}    
+

Exercise11_files/Problem1/Exercise1.sh

@@ -0,0 +1,28 @@
+###Align reference sequence files using muscle either format below is okay! Repeat alignment for all files.
+
+#Sigma
+/Users/lou/Desktop/muscle3.8.31_i86darwin64 -in sigma.ref -out sigma.align
+
+#transporter reference
+/Users/lou/Desktop/muscle3.8.31_i86darwin64 -in transporter.ref -out transporter.align
+
+#sporecoat
+/Users/lou/Desktop/muscle3.8.31_i86darwin64 -in sporecoat.ref -out sporecoat.align
+
+
+###Build a profile HMM using alignment sequences and hmmbuild.
+
+#Sigma
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmbuild sigma.hmm sigma.align
+
+#transporter reference
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmbuild transporter.hmm transporter.align
+
+#sporecoat
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmbuild sporecoat.hmm sporecoat.align
+
+
+###Search each proteome for sigma factors using hmmsearch.
+
+/Users/lou/Desktop/hmmer-3.1b2-macosx-intel/binaries/hmmsearch --tblout Results.txt $2 $1
+cat Results.txt >> All_Results.txt