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Comparing two gene lists for orthologs

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!

orthologs biopython
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updated by Biostar Biostar • written by Nitro_Shade • Nitro_Shade

Are these lists actual sequences or just gene names?

• 1 views • link
written by GenoMax GenoMax

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

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written by Nitro_Shade • Nitro_Shade

2 answers

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.

• 1 views • link
written by colindaven colindaven

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)
• 1 views • link
written by 5heikki 5heikki

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

• 1 views • link
written by Nitro_Shade • Nitro_Shade

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