OMA standalone has not listed splice variants used

Question

[nc52]

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

Answer 1

[Adrian Altenhoff]

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