Working on RNA-Seq data directed me to ask this question. In RNA-Seq jobs, after de novo assembly we have lots of transcripts with different rates of similarity (0 to almost 100 percent) that we sometimes don't know their loci.
So regardless of locus, on what reasons we differentiate two or more sequences?
How can we differentiate alleles of a gene from paralogous genes?
I hope my question is clear enough.