Question: Retrieve genes with more than N paralogs on ensembl
0
gravatar for corend
2.3 years ago by
corend70
corend70 wrote:

Is there a way on ensembl (or biomart?) to retrieve a list of gene IDs from a species that have more than N paralogs in this species?

I tried with biomart online but I didn't find any filters adapted.

ensembl gene genome • 731 views
ADD COMMENTlink modified 2.3 years ago by Jean-Karim Heriche21k • written 2.3 years ago by corend70
0
gravatar for Jean-Karim Heriche
2.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

You'll have to use the perl API for this. Something like this:

my @homologs = @{$Ensgene->get_all_homologous_Genes()};
my @paralogs = grep { $_->[2] eq 'homo_sapiens' && $_->[1]->description=~/paralog/ } @homologs;
ADD COMMENTlink written 2.3 years ago by Jean-Karim Heriche21k
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