True sequence type/orientation in a GenBank record?

Kevin Karplus karplus at bray.cse.ucsc.edu
Wed Jun 11 16:35:36 EST 2003


In article <8u26ev013fvgeb9mu9jn2qurhpjf6no0un at 4ax.com>, Peter Frank wrote:
> I am unsure about the following issue:
> Assuming I found a GenBank record with a sequence of interest and the
> definition line designates the sequence as mRNA or some other type of
> RNA, then is the sequence given really the RNA sequence or is it the
> sequence of the complementary cDNA?

If a sequence is labeled as RNA, then the sequence given should be
that of the RNA molecule, even if it was obtained by sequencing a
complementary DNA strand.  (That is, if the experimental technique
complements the strand, then it should be re-complemented before being
stored in the database.)

-- 
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Computer Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.




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