interpretation of orthofinder result

Question

[mxlsherry1992]

Dear all,

I found a setence in one paper

The orthologs and orthogroups between bottlenose catfish and channel catfish were generated using OrthoFinder (42). To obtain the species-specific genes, Protein BLAST (BLASTP) was performed in which genes not included in the orthogroups were queried against the genes in the orthogroups within the same species, with a maximal E-value of 1e-10. A reciprocal BLASTP with a maximal E-value of 1e-5 was used to query genes with no hits from previous steps (9). The genes with no hits to any orthologs were considered as species-specific genes.

But I am not sure what's the meaning of the BLAST part, orthofinder will give us multiple of files, so which files should be used for the BLASP? I will be pretty appreciated if you could give some guidance in detail :)

Thank you!!

[h.mon]

Unfortunately, only the authors of the paper will be able to provide guidance in detail, because the paper description of the analysis is not very detailed - maybe reference (9) has more details?

[mxlsherry1992]

Thanks! I will also email him!

Answer 1

[geneticatt]

It seems like they are taking genes from that weren't assigned to orthogroups and attempting to align them to the genes of the other species before calling them species specific. There is a file in the orthofinder output call 'Orthogroups_UnassignedGenes.csv' which contains the genes that would be used for the recipricol BLASTP in this method.

[mxlsherry1992]

Thanks for your kindly reply! But for the first step BLASTP with E-value 1e-10, will we also use the genes in "Orthogroups_UnassignedGenes.csv" file, to blast with the genes in orthogroups within same species? and for the reciprocal BLASTP step, we will also use the genes in orthogroups for the same species as first step, and then blast against thses genes with the genes have no hit from first step?

Thank u!!