Bioinformatics_Project - hjeon

Steps to run project

1. Pwd to bioinformaticsProject/ directory

2. Chmod execution privileges

chmod +x script.sh

3. Make sure muscle, hmmbuild, and hmmsearch commands are working as expected

4. Run script.sh

./script.sh

5. There will be two output text files "candidate.txt" and "table.txt" created after the run. "candidate.txt" saves best to worst candidates in order. "table.txt" saves search results for "proteome_xx hsp70_count mcrA_presence".

Errata

Using the default command in the form of "muscle -in seqs.fa -out seqs.afa" expends significant time and resources. script.sh had to adopt a new format of "muscle -in seqs.fa -out seqs.afa -maxiters 1 -diags -sv -distance1 kbit20_3" instead.