[Bioperl-l] How to merge mulitple genbank records into one record

[Brian Osborne]

Haiming,

Do the locations of the features refer to the individual 1000000 bp
sub-sequences or are they actually locations on the merged sequence, the
"chromosome"?

Brian O.


On 4/24/06 3:02 PM, "Haiming Wang" <hwang at uga.edu> wrote:

> Hi,
> 
> I am wondering if there is a script or tool can merge several genbank
> records into one record with all features' coordinates updated
> accordingly. For example, I have multiple Fugu scaffold_1 genbank files
> which are arbitrarily cut by 1000000 bps. I'd like to merge them into
> one big scaffold_1 genbank file.
> 
> Thanks in advance!
> 
> -Haiming
> 
> p.s. example data
> genbank record 1:
> LOCUS   scaffold_1 1000000 bp DNA HTG 8-FEB-2006
> DEFINITION  Fugu rubripes scaffold scaffold_1 FUGU4 partial sequence
> 1..1000000  reannotated via EnsEMBL
> ACCESSION   scaffold:FUGU4:scaffold_1:1:1000000:1
> ......
> //
> 
> genbank record 2:
> LOCUS  scaffold_1 1000000 bp DNA HTG 8-FEB-2006
> DEFINITION  Fugu rubripes scaffold scaffold_1 FUGU4 partial
> sequence1000001..2000000 reannotated via EnsEMBL
> ACCESSION   scaffold:FUGU4:scaffold_1:1000001:2000000:1
> ......
> //
> 
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