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Question: How to get distingushable CDS and UTR sequences of gene from biomart?
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gravatar for sohra
5.5 years ago by
sohra • 40
Switzerland
sohra • 40 wrote:

Hi all,

I would like to have CDS and UTRs sequences of some genes so that I cab distinguish CDS from UTR. I know there is such possibility in the UCSC  genome browser, which CDS and UTRs are shown in the upper case and lower case, respectively. Could you please let me know there isthe similar possibility in the biomart?
utr coding sequence biomart • 2.4k views
ADD COMMENT • link •
modified 5.5 years ago by Devon Ryan ♦ 98k • written 5.5 years ago by sohra • 40
0
gravatar for Devon Ryan
5.5 years ago by
Devon Ryan ♦ 98k
Freiburg, Germany
Devon Ryan ♦ 98k wrote:

Select "CDS start" and "CDS end" as attributes and then get the cDNA sequence. Things won't be upper/lower case, but the start/stop coordinates for the CDS will be in the header for each entry, so just parse that out.
ADD COMMENT • link written 5.5 years ago by Devon Ryan ♦ 98k

Thanks Devon,

I would be appreciated if you could clear me how parse the out as you mentioned "so just parse that out". Sorry if you found the question is basic, it's a big for me as a beginner.

ADD REPLY • link written 5.5 years ago by sohra • 40
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