Extract all members of particular gene family (including pseudogenes)

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9.7 years ago

Biomonika (Noolean) 3.2k

Hello,

I want to extract sequences of all members of particular gene family (including pseudogenes), together with the information about their strand. I like GeneCards (http://www.genecards.org/), but I cannot find the information about which release and coordinate system they are using. I also like biomart interface, but their latest release is GRCh37. GeneCards and biomart are definitely not using same coordinates and when I look at one particular gene, coordinates extracted from biomart look more reasonable. But even if I decide to use biomart, I will miss updates from the latest release and indeed, one of the genes I am interested in has 60bp longer sequence in RefSeq than in biomart.

Any advice how would you do this exercise? :)

genes coordinate • 2.1k views

ADD COMMENT • link updated 2.6 years ago by Ram 44k • written 9.7 years ago by Biomonika (Noolean) 3.2k

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BioMart is a data mining tool; it is not tied to any specific genome release. There are other implementations online which use GRCh38.

ADD REPLY • link 9.7 years ago by Neilfws 49k

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