You can use eutils to get the IDs programmatically and download the according Fasta files. However this will take some scripting.

If you have the Fasta file you can use makeblastdb that comes with the local blast installation to make a database out of the Fasta files.

Check http://www.biostars.org/post/show/518/how-to-download-all-est-sequences-for-organism-xx-from-ncbi/

Hi,

no, I don't have identifiers. I want to build it by taxonomic subdivision - PLN, or by keywords or other information, since taxon ids are sometimes wrong or absent.

Perhaps I could get a list of identifiers only from Entrez - I have not tried this for large lists.

Thanks.

update: no, there does not seem to be a way to output a list of identifiers from entrez (except one page at a time).

update: Entrez seems to have a 200 item limit on output via the browser

Thanks - I thought there must be a tool like eutils. Looks like I have to learn yet a nother scripting language and set of tools... jeez.

T.

Ok, I have tried to use this script:

http://www.ncbi.nlm.nih.gov/books/NBK25498/#chapter3.Application_3_Retrieving_large

but always get an empty output file and the script runs suspiciously quickly.

Any ideas?

Thanks,

T.

my IT dept. is blocking 'Get' use!! :(