Question: Locus_tag mapping between organisms based on homology
gravatar for Benni
10 days ago by
Benni20 wrote:

I basically have two related genomes with their respective locus tag list. Given the locus_tag of organisms 1, I want to find the closest (most homologe) locus_tag available in organisms 2. Including a qualitative measurement of the homology to filter the data. I would prefer homology based on protein level, but DNA level would be ok too. Since, the prokaryotic genomes are very closely related, there should be an obvious homolog for most genes. Do you know a tool, scipt, etc. for that?

locus_tag homology • 62 views
ADD COMMENTlink modified 10 days ago by h.mon13k • written 10 days ago by Benni20
gravatar for h.mon
10 days ago by
h.mon13k wrote:

Assuming you have predicted proteins from each genome, you can use PorthoMCL, OrthoMCL or OMA, among others.

As a side note, homology is a yes or no concept, there is no such thing as "most homologous". One of the measures to estimate homology is similarity, where we infer that the most similar genes / proteins are homologous.

ADD COMMENTlink written 10 days ago by h.mon13k
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