Question: How to find orthologs in both complete and fragmented genomes using OMA Standalone ?
0
gravatar for amandinette
2.0 years ago by
amandinette20
France
amandinette20 wrote:

Hi,

I would like to identify orthologs among about 40 bacterial genomes and then construct an orthologous matrix. Some of the genomes I am working on have been retrieved from the NCBI website and are complete. Others are custom genomes with an assembly level being "scaffolds".

I tried to use the "OMA Standalone" tool. I set "UseEsprit := true;" because of the fragmented assemblies of the custom genomes. It works until the end but no orthologous matrix was created at the end.

Is there a way to construct an orthologous matrix with both complete and fragmented genomes using OMA Standalone ?

Many thanks in advance if you can help me ! Best regards, Amandine

esprit oma orthologs • 794 views
ADD COMMENTlink modified 2.0 years ago by Christophe Dessimoz540 • written 2.0 years ago by amandinette20
2
gravatar for Christophe Dessimoz
2.0 years ago by
University College London
Christophe Dessimoz540 wrote:

Although OMA standalone and ESPRIT run within the same software, they have different purposes and for the moment we don't provide a unified pipeline between the two. This means that you have to take a two step process:

  1. Run ESPRIT to identify likely split genes (which is what you appear to have done). Based on the output—and I recommend starting by only considering the high-confidence "hits.txt" output file—generate a new fasta file with merged fragments. You need to do this last step by yourself—we currently don't provide a tool for this.
  2. Run the OMA algorithm (i.e. with UseEsprit := false) on the reference proteomes and updated fasta files with merged fragments. For this, you can keep the genomes that have not changed in the DB directory, and replace the scaffold-quality genomes (with filename .contig.fa) by their improved version from the ESPRIT output (make sure that the names are distinct).
ADD COMMENTlink written 2.0 years ago by Christophe Dessimoz540

Thank you for these explanations !

ADD REPLYlink written 2.0 years ago by amandinette20
1

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

ADD REPLYlink written 2.0 years ago by WouterDeCoster38k

done ! (sorry, I am a newbie on this forum :-) )

ADD REPLYlink written 2.0 years ago by amandinette20
1

Welcome to biostars. Interesting guidelines for posting can be found in the following posts:

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by WouterDeCoster38k
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