Question: Retrieving sequences from NCBI
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gravatar for JUAN MIGUEL MARIN DIAZARAQUE
11.4 years ago by
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. Best jm~ _______________________________ J. Miguel Marin http://www.est.uc3m.es/jmmarin Dep. of Statistics University Carlos III of Madrid Spain (E.U.)
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ADD COMMENTlink modified 11.4 years ago by Sean Davis21k • written 11.4 years ago by JUAN MIGUEL MARIN DIAZARAQUE70
Answer: Retrieving sequences from NCBI
0
gravatar for Marc Carlson
11.4 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi, You can use the biomaRt package to do stuff like this. http://www.bioconductor.org/packages/2.2/bioc/html/biomaRt.html Marc J. Miguel Marin 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. > > Best > > jm~ > > _______________________________ > > J. Miguel Marin > > http://www.est.uc3m.es/jmmarin > > Dep. of Statistics > University Carlos III of Madrid > Spain (E.U.) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENTlink written 11.4 years ago by Marc Carlson7.2k
Answer: Retrieving sequences from NCBI
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gravatar for Sean Davis
11.4 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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
ADD COMMENTlink written 11.4 years ago by Sean Davis21k
Answer: Retrieving sequences from NCBI
0
gravatar for Sean Davis
11.4 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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.) > _______________________________ > > >
ADD COMMENTlink written 11.4 years ago by Sean Davis21k
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