Question: Database Or Source For Paralogs Of A Particular Gene
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gravatar for Wayne
6.3 years ago by
Wayne1.0k
United States
Wayne1.0k wrote:

Hello all,

I'm wondering what the best source for paralogue information is. I want to use a gene as a query and receive a sequence list of closely related paralogous genes ( without orthologues). Does anyone know the best way to do this ? Its easy enough to find them manually for one gene, but as I'm looking to develop a high-throughput method I would like a dedicated source that can work as part of a script.

Cheers!

sequence alignment evolution • 3.3k views
ADD COMMENTlink modified 6.2 years ago by DG7.1k • written 6.3 years ago by Wayne1.0k
0
gravatar for PoGibas
6.3 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

Have you searched under the paralogues tag?

See "How to find paralogues?" question and accepted answers.

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by PoGibas4.8k
0
gravatar for Prakki Rama
6.2 years ago by
Prakki Rama2.4k
Singapore
Prakki Rama2.4k wrote:

have you come across Duplicated gene database before? Would that be useful?

ADD COMMENTlink written 6.2 years ago by Prakki Rama2.4k
0
gravatar for DG
6.2 years ago by
DG7.1k
DG7.1k wrote:

There isn't a perfect or all encompassing solution, because it depends a bit on what organisms you want included. Ensembl includes data for all of the organisms in their database, including inparalogs. You can Actually just use the BioMart part of Ensembl to construct the query and get everything back as a CSV file. But that only covers a fairly limited range of organisms unfortunately.

ADD COMMENTlink written 6.2 years ago by DG7.1k
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