bp_genbank2gff3.pl

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

bp_genbank2gff3.pl

anja
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: bp_genbank2gff3.pl

Don Gilbert-2-3

Anja,

I think you need to follow more of the Genbank format for your
made-up record.  In particular Linear/Circular in the Locus line,
accession,version lines, organism indent, very possibly some other fields.  
Maybe it would be easier for you to create GFF to start with.

- Don Gilbert

>From a full genbank record:
LOCUS       NC_001142             745745 bp    DNA     linear   PLN 12-MAR-2007
>> versus yours
LOCUS       Taro      5428 bp   DNA

DEFINITION  Saccharomyces cerevisiae chromosome X, complete chromosome
            sequence.
ACCESSION   NC_001142
VERSION     NC_001142.7  GI:116006492
>> versus yours
ACCESSION   none


KEYWORDS    .
SOURCE      Saccharomyces cerevisiae (baker's yeast)
  ORGANISM  Saccharomyces cerevisiae
            Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
            Saccharomycetales; Saccharomycetaceae; Saccharomyces.
>> versus yours
SOURCE      Colocasia esculenta
ORGANISM    Colocasia esculenta    
^^ missed indent; Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;


------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema