Retrieve genes with more than N paralogs on ensembl
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6.4 years ago
corend ▴ 70

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.

genome gene ensembl • 1.3k views
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6.4 years ago

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;
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