Question: Clusters proteins at each taxonomic rank - OMA
0
gravatar for anusblat
16 days ago by
anusblat0
anusblat0 wrote:

Hello everybody,

Anyone knows how to clusters proteins ( for example 90% of sequence identity) at each taxonomic rank (for example phylum) from an orthoXML file downloaded from OMA or other files. This will create non-redundant proteins in all taxomomic rank, but will avoid to loose a phylum that contain sequences.

Thanks! Alejandro

clustering oma • 86 views
ADD COMMENTlink modified 13 days ago by adrian.altenhoff650 • written 16 days ago by anusblat0
0
gravatar for adrian.altenhoff
13 days ago by
Switzerland
adrian.altenhoff650 wrote:

Hi Alejandro,

can you elaborate what you're trying to do? I'm one of the OMA developers, but I have a hard time to understand what you're doing.

In brief, OMA HOGs are groups of genes that all started diverging from a certain ancestral gene through speciation, so that gives you already gene clusters. If you want to subcluster them according to sequence identity, you would have to do that based on the available protein sequences. you could use pyham (https://github.com/DessimozLab/pyham) to extract the extent genes of any cluster you're interested.

ADD COMMENTlink written 13 days ago by adrian.altenhoff650
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1445 users visited in the last hour