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Old 07-01-2013, 03:39 AM   #1
rozitaa
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Default Annotation with refseq of transcripts

Hi,

I would like to annotate or add description to my transcript for which I only have refseq number (accession number). I cannot find any database which provides data for transcriptional refseq (e.g. "NM_000537"). Could you help me with finding that?

Best regards,
Rozita
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Old 07-01-2013, 04:39 AM   #2
GenoMax
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You can use the table browser from UCSC genome browser to do this. If you need help getting started with table browser look at this tutorial page: http://www.openhelix.com/ucscadv

Caveat: If your genome is not the list of supported genomes at UCSC then obviously this would not work.
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Old 07-01-2013, 04:44 AM   #3
dpryan
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You should be able to find the files to do this on the UCSC table browser (I think kgXref has some conversions). You can also check out Biomart, which might prove simpler. You can also do this in R with some of the Annotation databases, if your data happens to already be in R for whatever reason.

Edit: I should have refreshed before posting, GenoMax beat me to it!
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Old 07-01-2013, 06:49 AM   #4
rozitaa
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Thanks both. I found the table that I was looking for but I couldn't download it, so I just copied the webpage, presenting the table. Anyway now it's working.
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