[BioC] Retrieving sequences from NCBI

[Sean Davis]

On Fri, Jul 11, 2008 at 1:08 PM, J. Miguel Marin
<jmmarin at est-econ.uc3m.es> wrote:
>
> Thank you very much Sean,
>
> I have found also the command "getSEQ" from the library "annotate" from
> BioConductor.

Yep.  That will work.  Just keep in mind that you need to respect the
NCBI access limits (only during certain hours, and with a sleep() of
some seconds between calls; see the NCBI website for details) or they
WILL block access.  In other words, be very careful if using this type
of command in a loop.

Sean


>> On Wed, Jul 9, 2008 at 4:16 PM, J. Miguel Marin
>> <jmmarin at est-econ.uc3m.es> wrote:
>>>
>>> Dear users,
>>>
>>> I do not know whether this is a very simple question but I could not
>>> solve
>>> by myself...
>>> I would like to know if there exists in Bioconductor something like the
>>> matlab command "getgenbank". It serves to retrieve sequence information
>>> from
>>> the GenBank database in a simple way, and to download just the sequences
>>> to
>>> analyze them.
>>> I have seen the GEOquery and seqinr libraries but I could not download
>>> some
>>> given mitochondrial sequences.
>>
>> Eutils can be used for this.
>>
>> http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
>>
>> Sean
>>
>
>
>
>
> jm~
>
> _______________________________
>
>       J. Miguel Marin
>
> http://www.est.uc3m.es/jmmarin
>
>   Dep. of Statistics
> University Carlos III of Madrid
>       Spain (E.U.)
> _______________________________
>
>
>