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Problem: Given proteomes two strains of E. coli, e.g. in vivo versus in vitro. The proteins of the wildtype are mostly of unknown function but well documented for the in vitro strain.

Solution: proteinortho ecoli_lab_strain.faa ecoli_wildtype.faa In the output myproject.proteinortho.tsv can be used to further annotate the wildtype proteom.

Problem: Given a family of bacteria (e.g. 10 species). We want to find a core set of proteins that is conserved among the group of bacteria.

Solution: proteinortho input/*faa

Next we extract all proteins of the myproject.proteinortho.tsv for each species (the "core set")

for f in *faa; do proteinortho_grab_proteins.pl myproject.proteinortho.tsv $f > $f.core; done

(You can filter the myproject.proteinortho.tsv first e.g. select only groups with X species.)

Problem: Given the proteome and transcriptome of E. coli. Next we want to find the corresponding protein of each gene (or vice versa)

Solution: proteinortho -p=autoblast ecoli.proteins.faa ecoli.rna.fna

The output myproject.proteinortho.tsv contains all reciprocal best hits / groups between the proteome and the transcriptome. (autoblast automatically switches between tblastn and blastx)