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

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Sat Dec 25 08:15:53 EST 2004

You can try a sequence retreival API. If you find the fasta file, fastacmd
is a great way to access the individual sequenecs (used with formatdb).
Try using unipark90 if you can't find an up to date nrdb90.


On Sat, 25 Dec 2004 davidg at lsi.upc.edu wrote:

>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 
>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
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org

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