[BiO BB] Iterating over all the sequences in NR database

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Sun Dec 26 08:28:27 EST 2004


On Sat, 25 Dec 2004, Chris Dwan wrote:

>
>FASTA file:  				ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
>Formatted NCBI BLAST target:	ftp://ftp.ncbi.nih.gov/blast/db/nr.tar.gz
>
>-Chris Dwan
>  The BioTeam
>
>On Dec 25, 2004, at 8:11 AM, <davidg at lsi.upc.edu> wrote:
>
>> Hello.
>> Is there any way to access every element of the nr database, iterating
>> over all the sequences in that database? I thought about getting the

By the way, the default behaviour of blast is to search all the sequences
in the database.

Best,
dan.


>> nr database in a FASTA format text file which contained every protein
>> in the nr database, but i haven't found it. And even if I did, i don't
>> know if there's a better option.
>> Thank you.
>>
>>
>> --
>> David García Cortés
>> Instituto Nacional de Bioinformática (INB)
>> Nodo Computacional GNHC-2 UPC-CIRI
>> c/. Jordi Girona 1-3
>> Modul C6-E201                   Tel.  : 934 011 650
>> E-08034 Barcelona               Fax   : 934 017 014
>> Catalunya (Spain)               e-mail: davidg at lsi.upc.edu
>>
>>
>>
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