Comparing two gene lists for orthologs

Question

[Nitro_Shade]

Hi there!

An ongoing project of mine requires me to compare two gene lists (that come from different organisms) and find out the extent of overlap - this includes orthologs.

Any existing tool that can do this?

If not, I was thinking of writing a script that does this for me. However, I'm new to BioPython (and BioPerl) and would greatly appreciate it if someone could tell me a way to extract orthologs from KEGG using a gene symbol.

Thanks in advance!

[GenoMax]

Are these lists actual sequences or just gene names?

[Nitro_Shade]

These are gene names. Getting sequences will not be a hassle, though.

Answer 1

[colindaven]

Ok. I would recommend the tool proteinortho for a simple multicore ortholog finder.

Get the gene/protein sequences, make sure the headers are unique and map them to each other. The main output is a simple TSV.

[Nitro_Shade]

Thanks! I'll try it out.

Answer 2

[5heikki]

Assuming the genes have the same names in both organisms:

comm -1 -2 <(sort list1.txt) <(sort list2.txt) > lines_that_appear_in_both_files

man comm
..
       -1     suppress column 1 (lines unique to FILE1)
       -2     suppress column 2 (lines unique to FILE2)

[Nitro_Shade]

They don't. That's why I need to access orthologs :)