tools for finding paralogues

Question

[ayeshamaqsood93.am]

Which tool can be used to find the paralogues of a specific gene, other than HUGO. Please help me finding one it would be of great help.

[lieven.sterck]

if you're up to doing a independent analysis: inparanoid or orthomclor ...

[Andrzej Zielezinski]

What organisms do you work on?

Answer 1

[Carambakaracho]

good old COG of the Koonin group must be doing this: https://sourceforge.net/projects/cogtriangles/

[Carambakaracho]

a short web search yielded a quite comprehensive review on this, dating from 2017 and mentioning the tools lieven cited above:

Nichio BTL, Marchaukoski JN, Raittz RT. New Tools in Orthology Analysis: A Brief Review of Promising Perspectives. Front Genet. 2017;8:165. Published 2017 Oct 31. doi:10.3389/fgene.2017.00165

I'm surprised nobody adopted diamond to replace blast for the computational challenge of reciprocal best blast hits... any opinions on this?

[lieven.sterck]

yes, since most of those tools use (some) of blast output stats, it is not highly advisable to use the DIAMNOND ones as those are remarkably different . (my personal two cents though ;) )

[Carambakaracho]

ah thanks - I didn't do a in depth comparison yet and my first impression was that despite some differences, the stats where rather comparable. I'll need to have a closer look at this someday

Answer 2

[Erin Haskell]

If you know the gene name (i.e. the HGNC symbol), or a stable ID of the database you can use Ensembl to find the paralogues. Here is an example for the gene MCM6. If you want further help with browsing Ensembl for comparative genomics data you can watch our YouTube comparative genomics videos which have been recently updated. If you have a list of genes you want to find paralogues for then you will want to use BioMart - there's a short video for this too in the previous link.