Definition of CDS and ORF

John Hill jh5f+ at andrew.cmu.edu
Wed Apr 4 20:17:38 EST 1990


While preparing sequence submissions for GenBank, I was perplexed by
the following questions.  Should the 3' limit of a CDS (= coding
sequence) include the last nucleotide BEFORE the stop codon or the
last nucleotide OF the stop codon?  Does ORF (=open reading frame)
have the same definition?  In a small sampling of local opinions and
different sequence analysis software, there is no consensus (with
approximately a 50:50 split).  Does a rigorous definition exist?  If
not, is there a general consensus?

John Edward Hill                      Dept. of Biological Sciences
Internet: jh5f+ at andrew.cmu.edu        Carnegie Mellon University
Bitnet:   jh5f+ at andrew.bitnet         4400 Fifth Avenue
412-268-5122                          Pittsburgh, PA.  15213-3890  USA



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