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Bioperl or ncbi: parsing refseq filesby roibrodo (Sexton)
|on Jun 14, 2010 at 13:51 UTC||Need Help??|
roibrodo has asked for the
wisdom of the Perl Monks concerning the following question:
I have downloaded some large RefSeq files (Genbank format, i.e. both sequence and annotations; e.g. http://www.ncbi.nlm.nih.gov/nuccore/NC_002945.
I want to get a part of that sequence along with its annotations - exactly as I do online using the "Change region shown" window on the right - then dump this as a (smaller) Genbank file. Very simple... but I couldn't figure out how to do that.
one way of achieving this is using seqret from emboss: e.g. seqret -sformat1 gb -sequence "in_seq.genbank" -sbegin 10000 -send 50000 -feature -outseq out_seq.genbank.genbank -osformat2 gb
Thanks to vinnana from the bioperl community!