Question: How to find orthologs in both complete and fragmented genomes using OMA Standalone ?
0
gravatar for amandinette
8 months ago by
amandinette10
France
amandinette10 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 • 309 views
ADD COMMENTlink modified 8 months ago by Christophe Dessimoz420 • written 8 months ago by amandinette10
2
gravatar for Christophe Dessimoz
8 months ago by
University College London
Christophe Dessimoz420 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 8 months ago by Christophe Dessimoz420

Thank you for these explanations !

ADD REPLYlink written 8 months ago by amandinette10
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 8 months ago by WouterDeCoster24k

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

ADD REPLYlink written 8 months ago by amandinette10
1

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

ADD REPLYlink modified 8 months ago • written 8 months ago by WouterDeCoster24k
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