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Re: Bioperl or ncbi: parsing refseq files

by david_lyon (Sexton)
on Jun 14, 2010 at 18:33 UTC ( #844699=note: print w/ replies, xml ) Need Help??


in reply to Bioperl or ncbi: parsing refseq files

If I was doing this which I have done a million times you want to use one if the emboss packages which can parse out the features and sequences that you are interested in or spit out the features in a table format so you can upload them into a db or parse them on the fly. eg: http://emboss.sourceforge.net/apps/release/6.2/emboss/apps/extractfeat.html
I would avoid using bioperl for this.


Comment on Re: Bioperl or ncbi: parsing refseq files
Re^2: Bioperl or ncbi: parsing refseq files
by roibrodo (Sexton) on Jun 15, 2010 at 09:36 UTC

    Thanks for the reply.

    I read some of the documentation but did not find an appropriate example.

    Would you be kind enough to let some hints on how to get from a GenBank file to a smaller GenBank file containing some range of the sequence? It will really help getting stated with emboss (I think examples are a great way to start experimenting)

    Thanks!

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