Question: OMA standalone has not listed splice variants used
gravatar for nc52
5 weeks ago by
nc5210 wrote:

Hi there,

This is just a small question I hope! My OMA run has completed and I appear to have all of the files I am supposed to have in the Output directory bar one: used_splicing_variants.txt.

I specified in parameters.drw "UseOnlyOneSplicingVariant := true;" and provided the splicing information for each genome in DB as specified in the manual....

i.e. genome1.fa, genome1.fa.splice, genome2.fa, genome2.fa.splice etc

7 of the 9 genomes we are investigating have detailed splicing information, 1 has very limited and the remaining genome has precisely 0. The .splice files were provided for each with an empty one for the genome where this information was not available.

In this case - has OMA defaulted to inferring alternative splicing variants as paralogs?

Many thanks, Nicki

oma • 81 views
ADD COMMENTlink modified 27 days ago by adrian.altenhoff610 • written 5 weeks ago by nc5210
gravatar for adrian.altenhoff
27 days ago by
adrian.altenhoff610 wrote:

Hi Nicki,

yes, for genomes that do not have splicing information, all the protein sequences are treated as independable genes and are most likely inferred as paralogs. One reason why they might not is due to very different lengths, in which case OMA might decide not to call them as orthologs/paralogs.

Best wishes, Adrian

ADD COMMENTlink written 27 days ago by adrian.altenhoff610
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