BioinformaticsProject.Answer

#Creating the Muscle for hspGenes
cd ~/Private/bioinformaticsProject/ref_sequences | cat hsp70gene_*.fasta >> hspgenes.txt | ~/Private/Biocomputing2022/tools/muscle -in hspgenes.txt -out hspGenesmuscle.txt
#HmmBuild for hspGenes
~/Private/Biocomputing2022/tools/hmmbuild hmmbuild.hsp hspGenesmuscle.txt
#Copy hmmbuild.hsp  to Proteome Directory
cp hmmbuild.hsp ../proteomes
#Move to Proteomes Directory to Run for loop
~/Private/bioinformaticsProject/proteomes
#HmmSearch for hspGenes For Loop
for file in proteome_*.fasta
do
	~/Private/Biocomputing2022/tools/hmmsearch --tblout hmm.hspSearch${file} hmmbuild.hsp $file
done



#Creating the Muscle for the mcrAgenes
cd ~/Private/bioinformaticsProject/ref_sequences | cat mcrAgene_*.fasta >> mcrAgene.txt | ~/Private/Biocomputing2022/tools/muscle -in mcrAgene.txt -out mcrAmuscle.txt
#HmmBuild for mcrAgenes
~/Private/Biocomputing2022/tools/hmmbuild hmmbuild.mcrA mcrAmuscle.txt
#Copy hmmbuild.mcrA to Proteomes Directory
cp hmmbuild.mcrA ../proteomes
#Move to Proteomes Directory to Run For Loop
~/Private/bioinformaticsProject/proteomes
#HmmSearch for mcrA gene For Loop
for file in proteome_*.fasta
do
	~/Private/Biocomputing2022/tools/hmmsearch --tblout hmmSearch.mcrA${file} hmmbuild.mcrA $file
done