[Bioperl-l] RE: Bio::SeqIO

[Qi, Yanping]

Hi Ewan;

Thanks for your response.  I have two more observations regarding the
converted GenBank format:
1). LOCUS field.  Genbank has fixed positions for information contained in
the LOCUS record.  I found the Bio::SeqIO converted GenBank format does not
follow the rule.  Here is the detailed format for the LOCUS record:
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Positions       Contents
1-12    LOCUS
13-22   Locus name
23-29   Length of sequence, right-justified
31-32   bp
34-36   Blank, ss- (single-stranded), ds- (double-stranded), or
         ms- (mixed-stranded)
37-40   Blank, DNA, RNA, tRNA (transfer RNA), rRNA (ribosomal RNA), 
        mRNA (messenger RNA), or uRNA (small nuclear RNA)
43-52   Blank (implies linear) or circular
53-55   The division code (see Section 3.3)
63-73   Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

2). The ORIGIN field.  There should be 6 more space following "ORIGIN"
keyword.  

Thanks for your attention in advance.

Yanping
  

> -----Original Message-----
> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> Sent: Tuesday, April 17, 2001 2:16 PM
> To: Qi, Yanping
> Cc: bioperl-l@bioperl.org
> Subject: Re: Bio::SeqIO 
> 
> 
> 
> 
> On Tue, 17 Apr 2001, Qi, Yanping wrote:
> 
> > Hi;
> > 
> > I am using the Bio::SeqIO module to convert a EMBL file to 
> Genbank format.
> > I have found the DR (database crossreference) section did 
> not appear in the
> > Genbank file.  Does the DR section get converted?  
> 
> I don't think GenBank do DR lines (or equivalent) in the main 
> part of the
> files, they just do dbref's in the features. 
> 
> 
> Does anyone have any insight here on the list? I am not a 
> genbank format
> expert.
> 
> 
> > 
> > Thanks in advance.
> > 
> > Yanping
> > 
> >  
> > ------example of the DR section-----------
> > XX
> > DR   SPTREMBL; P57168; P57168.
> > DR   SPTREMBL; P57170; P57170.
> > DR   SPTREMBL; P57192; P57192.
> > DR   SPTREMBL; P57213; P57213.
> > XX
> > 
> > 
> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
>