In-paralog & out-paralog

Question

[397975944]

Hi, I'm trying to find the ortholog of protein A of species 1 in species 2 using BLAST. We also find additional homologs in species 2. Can we decide whether they are in-paralog or out-paralog using BLAST alone, or do we have to build the phylogenetic tree first?

Answer 1

[Dave Carlson]

Blast alone cannot tell you what kind of homology relationship two proteins share. Some researchers use reciprocal best hits as proxy for orthology (e.g., this paper), but this is more out of convenience than anything else.

If at all possible, I would try a tool like Orthofinder that is at least attempting to explicitly determine orthology and paralogy among your homologous proteins.

[397975944]

This is the schematic diagram of in-paralogs and out-paralogs provided in the lecture. The question only say design a strategy to distinguish in-paralogs and out-paralogs using BLAST. I'm wondering if the green circles are in-paralog and originated before species split, can we say that circle 1-4 from mouse will be orthologs to circle 7-10 in chicken and we cannot find orthologs of 5&6 in chicken?

[Dave Carlson]

The green circled proteins duplicated in the common ancestor of the species in question, so they are out-paralogs. While the blue circled proteins duplicated in mouse after its lineage split from both human and chicken. Therefore, with respect to their relationships with the chicken and mouse P protein, these blue proteins are in-paralogs.

I believe these terms were introduced in this paper.

Using blast alone, I'm not sure how one would determine whether a particular protein copy would be considered an in-paralog or out-paralog without making some rather questionable assumptions about things like rates of sequence divergence.

But that caveat aside, you might want to think about the evolutionary relationships between the various homologous proteins and make some reasonable guesses about the different levels of sequence similarity we might expect to see in in-paralogs and out-paralogs relative to protein P.