Comparing two gene lists for orthologs
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8.4 years ago
Nitro_Shade ▴ 30

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 • 2.1k views
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Are these lists actual sequences or just gene names?

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

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8.4 years ago

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.

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Thanks! I'll try it out.

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8.4 years ago
5heikki 11k

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

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