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Re: NCBI sequence fetching

by citromatik (Curate)
on May 12, 2009 at 08:59 UTC ( #763440=note: print w/replies, xml ) Need Help??


in reply to NCBI sequence fetching

Instead of Bioperl you can try NCBI's eutils. In particular the EFetch tool to retrieve fasta sequences given a list of accession identifiers

citromatik

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Re^2: NCBI sequence fetching
by capemaster (Initiate) on May 12, 2009 at 09:34 UTC
    Thank you... Tha fact is that with eFetch I don't know how to start :D

    Can you help me on this aspect?
    Stefano

      In the eutils help page you can find a sample Perl program that you can download and execute locally. Try to understand what it does, and then try to modify it to fits your purposes.

      If you have any problem in the process, do not hesitate to post a new question here

      Hope this helps

      citromatik

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[stevieb]: I've finally added the ability for berrybrew to fetch the list of perls available directly from Strawberry's releases.json file. Instead of pulling from there on every single call, I've added a berrybrew fetch, so it's only updated..
[stevieb]: ...on request. There's some supporting work I need to do, as well as update the docs, but it's in the v1.12 branch if anyone wants to play with it...
[stevieb]: ...issue 62 will track what else needs to be done.

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