[Bioperl-l] to retrieve Upstream and downstream genes -Reg

Carnë Draug carandraug+dev at gmail.com
Wed May 2 10:20:49 EDT 2012


On 2 May 2012 14:14, tarakaramji M <tarakaramji at gmail.com> wrote:
> Dear all,
> I am new to use bioperl modules. Could please guide me retrieving the
> upstream and downstream genes of a operon if a set of sequences or
> Accession numbers are given.
> Thanks in advance

Hi Tarak,

Look into the bp_genbank_ref_extractor script (which is already in
bioperl https://github.com/bioperl/bioperl-live/blob/master/scripts/Bio-DB-EUtilities/bp_genbank_ref_extractor.pl
). You can configure how much downstream and upstream base pairs to
get, just read the documentation.


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