[Bioperl-l] GenBank format and feature names > 15 char

Lincoln Stein lstein at cshl.edu
Mon Jan 14 13:53:15 EST 2008


Hi Scott,

He is correct about the limitation, but we deliberately relaxed it because
we were running into situations where we lost information during
roundtripping from other formats into genbank.

Lincoln

On Jan 14, 2008 1:46 PM, Scott Cain <cain.cshl at gmail.com> wrote:

> Hi all,
>
> Last month, I got a bug report on the GBrowse bug tracker:
>
>
> http://sourceforge.net/tracker/index.php?func=detail&aid=1845217&group_id=27707&atid=391291
>
> about a problem with dumping invalid GenBank files.  GBrowse uses
> Bio::SeqIO::genbank to create these dumps.
>
> In his bug report, he claims that feature names over 15 characters long
> are invalid, and provided and example GenBank file where a feature is
> named 'BAC_cloned_genomic_insert', which is over 15 characters.  What I
> want to know is this: is this truly a restriction on the GenBank format,
> or is it a software problem with some other package?  Do we need to fix
> genbank.pm?  I'm perfectly willing to do it; I'm just hesitant to
> believe this is really a bug.
>
> Thanks,
> Scott
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   cain.cshl at gmail.com
> GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> Cold Spring Harbor Laboratory
>
>
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Lincoln D. Stein
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