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When to decide that two similar sequences are different genes or not?
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18 months ago
utsafar • 20

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 (somme times) 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 paraloge genes?

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How can we differentiate alleles of a gene

Relevant recent discussion: Does allele refer to the entire gene sequence or one position of the gene sequence?

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I think this is a different question. There he wants to know the what is the exact definition of "allele". I know what is an allele, I want to know how to differentiate between alleles and paralogs in an RNA-Seq assembley.

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Just wanted to point out that "alleles of a gene" terminology is conceptually incorrect. Your question is fine other than that. Perhaps you meant to say orthologs?

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I assume you don't have a reference genome of the organism you are working on?

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