[Bioperl-l] Add sequence feature

Roy Chaudhuri roy.chaudhuri at gmail.com
Fri Aug 13 11:57:27 EDT 2010


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You can loop over the features in your Bio::Seq object:
for my $feat ($seq->get_SeqFeatures) { # do something }

And once you have found the feature you want to modify, you can add a 
tag using something like:
$feat->add_tag_value('note',"this is a note");

When you're finished you can write out the modified sequence object to a 
new GenBank file.

On 13/08/2010 16:40, Jessica Sun wrote:
> no i want to load the genbank file with existing features and I need to
> add some new feature tags to the existing ones and then save to a new
> update genbank file for local usage. I just not quite good on how to
> easily merge the two steps you recommended into one in a neat way.
>
> thx
>
>
> On Fri, Aug 13, 2010 at 11:37 AM, Roy Chaudhuri <roy.chaudhuri at gmail.com
> <mailto:roy.chaudhuri at gmail.com>> wrote:
>
>     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>
>         <mailto: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
>
>
>
>
>
> --
> Jessica Jingping Sun



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