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Inconsistent use of "/codon_start=" qualifier at EMBL

Conrad Halton Halling chh9 at quads.uchicago.edu
Tue Sep 1 20:55:28 EST 1992


I am writing a program that parses the CDS keys of the FEATURE tables
of GenBank and EMBL entries.

I have discovered an inconsistent use of the "/codon_start=" qualifier in
several EMBL entries.

On page 55, "The DDBJ/EMBL/GenBank Feature Table: Definition" manual
(version 1.04) states that the "/codon_start=" qualifier can take values
of 1, 2, or 3 (indicating the relative offset of the reading frame from
the start nucleotide).  However, as in the example below, the qualifier takes
the value of the actual position in the sequence.  (I believe this was the
meaning implied for this qualifier in version 1.03 of the feature table
definition.)  I have not yet observed this problem in GenBank entries.

This sort of thing doubles the work of the programmer, who must test for
both eventualities.

Is this something that will be corrected soon?

Example:
--------

[SSCYS]     Synechococcus sp. cysA, 3' end, spbA, cysT, orf81, cysR, and cysW
     genes, complete cds.

ID [LOC]
     SSCYS      standard; DNA; PRO; 4127 BP.

ACCESSION [ACC]
     M65247;

[ ... several lines omitted ... ]

FEATURES [FEA]
     Key             Location/Qualifiers
     CDS             complement(<1..33)
                     /note="homologous to nucleotide binding
                     polypeptides of other permease systems"
                     /gene="cysA" /codon_start=33
     CDS             233..1285
                     /function="sulfate-binding protein" /gene="sbpA"
                     /codon_start=233
     CDS             1360..2196
                     /note="integral membrane polypeptide of the
                     sulfate permease" /gene="cysT" /codon_start=1360
     CDS             2220..2465
                     /label=orf81                /codon_start=2220
     CDS             2493..3113
                     /gene="cysR"                /codon_start=2493
     CDS             3159..4019
                     /note="integral membrane polypeptide of the
                     sulfate permease" /gene="cysW" /codon_start=3159


-- 
Conrad Halling
c-halling at uchicago.edu




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