Dear Friends, Hi (I am not native in English)
I want to launch some Ortholog comparison between some candidate gene of my species of interest and Danio rerio (zebrafish).
I have found similar approach in this paper under the section: "Ortholog comparison between A. sinensis and Danio rerio" but it is not clear to me which software they have used?
They have searched the orthologs of 11 genes in three gene families (sox, apolipoprotein and cyclin) in two previusly mentioned fishes.
1- Which software is better for this comparison?
2- Where I could collect the orthologs of these 11 genes ? (did I must collect their proteins? or nucleotides from some Zebrafish database ?)
3- How I must offer my set of genes (I mean the genes of my newly sequenced transcriptome) to compare with?
Maybe I must use all the transcriptome assembly or its translation ? (it seems that OrthoFinder needs proteins)
Thank you in advance
NOTE: my data are from RNA-seq and de novo assembly. I also use Transdecoder to translate longest ORF for each isoforms.