Ncbi Database Extract A Gene From Gene Bank Perl

Question

[Freemira]

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

[Damian Kao]

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?

[Neilfws]

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?

[Freemira]

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

[Freemira]

@DK yes that's it

Answer 1

[Damian Kao]

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

[Freemira]

I need it in just perl

[Neilfws]

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.

[Freemira]

yep it's a homework ..

[Pierre Lindenbaum]

so, what did you try so far ?

[Freemira]

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

Answer 2

[Pablacious]

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 ;-).

Answer 3

[Michael Schubert]

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