CO2: Format: CSV CAMPEP,LogFC,logCPM Keep a header, the script will ignore the first line and assign new headers

BLAST Query- the last part of the identifier must be “|unique_name” blastp -db _.pep.fa -query _genesofinterest.txt -out {species_name}_genetype_blast.csv -outfmt “6 evalue qseqid ppos sseqid” Columns will not have name but they are: Evalue,query sequence ID, percent match, sequence id The script will give the file column names HMM Create seed files

MAFFT Version 7 takes in seed file and gives alignment file navigate to where you want the aligned file to rest mafft gene_seed.txt>gene_seed_aln.txt

HMM build from MAFFT takes in aligned file from above and makes hmm file navigate to gene_type folder @CF goes to .exe file output input ../hmmbuild OMT.hmm gene_seed_aln.txt

HMM Search takes hmm file from above navigate to gene_type folder @CF for GOC goes to .exe file out 1 file out 2 input hmm input pep.fa ../hmmsearch -o OMT_hmmout.csv --tblout test.csv OMT.hmm ../PEPfa/Goc.pep.fa

#####without CO2 from MMETSP website

Part I: PEP_HMM1.py This is a bash file. Input: the name of species (group of organisms) from MMETSP Output: HMM profiles for CCM and Photorespiration genes, counts from MMETSP

Part II: PEP_HMM2.ipynb This script must be run on some python interface. Cannot run on shell because a function from pandas is not compatible with bash.

Make sure this script is in the same folder as the output from part I.

Input: the name of species (group of organisms) from MMETSP (same as in part I) Output: Table with genes that map to CCMs and photorespiration for all the species in the group you selected.