Question

tools for finding paralogues

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5.5 years ago

ayeshamaqsood93.am • 0

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.

paralog • 1.7k views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 5.5 years ago by ayeshamaqsood93.am • 0

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

ADD REPLY • link 5.5 years ago by lieven.sterck 15k

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What organisms do you work on?

ADD REPLY • link 5.5 years ago by Andrzej Zielezinski 11k

score 0 · Answer 1 · 2018-11-09

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5.5 years ago

Carambakaracho ★ 3.2k

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

ADD COMMENT • link 5.5 years ago by Carambakaracho ★ 3.2k

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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?

ADD REPLY • link 5.5 years ago by Carambakaracho ★ 3.2k

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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 ;) )

ADD REPLY • link 5.5 years ago by lieven.sterck 15k

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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

ADD REPLY • link 5.5 years ago by Carambakaracho ★ 3.2k

score 0 · Answer 2 · 2018-11-09

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.