Dear Friends, Hi ( I'm not native in English so, be ready for some possible language flaws)
(Please modify the title if it is not clear, and sorry if it is duplicated question)
In the search for some candidate genes in my fish de novo transcriptome assembly, I have downloaded my selected genes sequence (NCBI/Nucleotide section) from different fish species for each gene (why? because there was was several representative in the fish taxa) and create a collection.fasta file. Then I have used
makeblastdb command with the -
dbtype nucl to convert my assembly.fasta to a searchable database.
Then I have used
BLASTN (evalue=1e-6) and used my collection.fasta as query and assembly.fasta as database.
In the blastn result, I have:
"TRINITY_DN110178_c1_g2_i5" map to "Acipenser ruthenus -> Androgen receptor" (gb|KF765735.1)
TRINITY_DN98381_c0_g1_i2" map to "Larimichthys crocea -> Androgen receptor" (gb|GU479047.1)
This is my question:
What is it telling us ?
We have two separate Transcripts(genes) for the same thing (here : androgen receptor). Why is that and what that show?