Consider using Nentrcmd, which is a command line interface to Entrez
which is available as part of the NCBI toolkit:
Once you have built the 'makeall' portion of the toolkit (see the
README), you can build Nentrcmd using:
make -f makenet.unx Nentrcmd
A few other compiler-related options may be necessary.
Once you have built Nentrcmd for your system, you can get short online
or longer help via:
Nentrcmd -h -p manual
Official help is available from toolbox at ncbi.nlm.nih.gov, but I may be
able to offer some help as well. I'm the author of this program, which
was used as the retrieval engine for the original version of WWW Entrez
Timothy M. Kunau (CBC) wrote:
>> We cannot be the only group asking this question,
>> We need to automate the download of sequences and updates from NCBI.
> They do provide a web interface:
>>http://www.ncbi.nlm.nih.gov/Entrez/batch.html>> We have looked at nclever. For various reasons, this has been
>> What other methods are available to download sequences in a batch form?
> Timothy M. Kunau kunau at ahc.umn.edu Computational Biology Ctrs.
> Genomic Database Administrator, Computing and Bioinformatics, AHC
> 612-626-6937 http://www.cbc.umn.edu/~kunauhttp://www.cbc.umn.edu