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Ncbi Database Extract A Gene From Gene Bank Perl

how can we extract a gene from Genbank file using the e-utilities of ncbi in perl not bioperl? ?

perl genbank ncbi homework
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updated by Michael Schubert Michael Schubert • written by Freemira • Freemira

Do you mean you want to extract the sequence from a genebank file that you've obtained using the NCBI e-utilities. And you want to extract the sequence using perl?

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written by Damian Kao Damian Kao

Please improve this question. When you say "extract gene from Genbank file", it implies that you want to parse a file and extract information, such as a sequence. When you say "using e-utilities", it sounds as though you want to download the Genbank file for a particular gene from NCBI. So which is it?

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written by Neilfws Neilfws

it's download the genbank file for a particular gene from ncbi

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written by Freemira • Freemira

3 answers

BioPerl has extensive e-utilities capabilities: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

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updated by Ram Ram • written by Damian Kao Damian Kao

Why "just perl"? The point of libraries like BioPerl is to make your life easier by not "reinventing the wheel". Unless of course this is a homework problem.

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written by Neilfws Neilfws

@pierr Lindenbaum I'm searching the ncbi e-utilites

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written by Freemira • Freemira

Given that this is a homework I'll only give you a tip: NCBI eBot.

Find it and try to use it, I'm sure it will give you something useful ;-).

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written by Pablacious Pablacious

http://www.ncbi.nlm.nih.gov/books/NBK25501/, particularly the efetch part.

This is roughly one page to read. I suggest you do it yourself (there is even a url-encoded example).

I'm sure the Perl part is sufficiently covered in your lecture slides. You could also use pablacious' suggestion to cheat ;-)

edit: oh, and if you have further problems please post your code, so we can see that you actually tried

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written by Michael Schubert Michael Schubert

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