[Bioperl-l] Add sequence feature

Roy Chaudhuri roy.chaudhuri at gmail.com
Fri Aug 13 11:37:20 EDT 2010


I'm not sure I understand, do you mean that you want to load just the 
sequence from the GenBank file (ignoring the existing annotation), then 
add your own features? There are instructions on how to do that here:
http://www.bioperl.org/wiki/HOWTO:SeqIO#Speed.2C_Bio::Seq::SeqBuilder

On 13/08/2010 16:27, Jessica Sun wrote:
> unfortunately. I want to add the feature to the sequence object I got
> from the Genbank file, I do not mind to save a new genbank file but
> these new genbank file contains the original genbank format and info I
> got plus the new feature tags I need to added to. Any quick solution to
> this?
>
> thx
>
> Jessica
>
>
>
> On Fri, Aug 13, 2010 at 11:21 AM, Roy Chaudhuri <roy.chaudhuri at gmail.com
> <mailto:roy.chaudhuri at gmail.com>> wrote:
>
>     Hi Jessica.
>
>     You need to use Bio::SeqIO to read in the GenBank file to a BioPerl
>     sequence object, and to write your new GenBank file:
>     http://www.bioperl.org/wiki/HOWTO:SeqIO
>
>     To add a new feature follow the instructions here:
>     http://www.bioperl.org/wiki/HOWTO:Feature-Annotation#Building_Your_Own_Sequences
>
>     (except that you are adding the feature to the sequence object you
>     got from the Genbank file, not a new Bio::Seq object).
>
>     Cheers.
>     Roy.
>
>
>     On 13/08/2010 16:06, Jessica Sun wrote:
>
>         Does anyone knows how to open a genbank file, add new feature
>         and then save
>         a new genbank
>         file with new feature added in bioperl ?
>
>         thx
>
>
>
>
>
> --
> Jessica Jingping Sun



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