[Bioperl-l] RE: strand in Meta-data sequence-region

Roels, Steven Steven.Roels at mpi.com
Thu Jul 15 21:36:38 EDT 2004


The recent discussion of GFF3 parsing on the bioperl list reminded me
about a request I made for strand info in the sequence-region meta-data
line (to handle "flipped" slices).

Not urgent - just thought I'd point it out while folks are working on
the relevant modules...

Or did something come up that indicated the suggested change was a bad



>>Sent: Tuesday, January 20, 2004 7:14 AM
>>To: Roels, Steven; gff-list at sanger.ac.uk
>>Subject: Re: spaces definition
>>Hi Steven,
>>I missed your messages due to spam filter screw up.  With respect to
>>your first question about the strand, I will be happy to add an
>>optional strand field (plus strand assumed if missing).  Does that
>>sound OK?
>Perfect - thanks.
>>>-----Original Message-----
>>>From: owner-gff-list at sanger.ac.uk
[mailto:owner-gff-list at sanger.ac.uk] On
>>>Behalf Of Roels, Steven
>>>Sent: Friday, December 12, 2003 10:21 AM
>>>To: gff-list at sanger.ac.uk
>>>Subject: strand in Meta-data sequence-region
>>>Hello all,
>>>The spec that I see (http://song.sourceforge.net/gff3.shtml) lists
>>>following for the sequence-region meta-data tag:
>>>##sequence-region seqid start end
>>>        The sequence segment referred to by this file, in the format
>>>        "seqid start end".  This element is optional, but strongly
>>>        encouraged because it allows parsers to perform bounds
>>>        checking on features. There may be multiple ##sequence-region
>>>        directives, each corresponding to one of the reference
>>>        sequences referred to in the body of the file.
>>>Shouldn't "strand" be included as well? I'm often playing with
>>>gene-centered slices that have been flipped as needed so that the
>>>of interest is oriented low to high. Without strand here, I can't
>>>sequence region accurately in the GFF file. Or is there some other
>>>to do it that I'm missing?

This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged.  This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else.  If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender.  Thank you.

More information about the Bioperl-l mailing list