[Bioperl-l] loading sprot.dat

Juguang Xiao juguang at tll.org.sg
Fri Jan 9 03:59:07 EST 2004

On Thursday, January 8, 2004, at 11:18  pm, Robinson, Peter wrote:

> Hi all,
> I would like to load the contents of the Swiss-Prot file sprot.dat 
> into a mysql database. Since I have a relatively specific question, I 
> would like to use a databse of my own design and just extract portions 
> of the relevant entries from sprot.dat rather than the whole thing.

Do you know biosql and bioperl-db projects? I am not sure why you use 
your own database schema, rather than biosql one. Is biosql schema 
missing something so that it cannot satisfy your requirement? Please 
let Hilmar and us know if so.

bioperl-db/scripts/biosql/load_seqdatabase.pl can load Swissprot into 
mysql. I have load the whole SP months ago. There is option called 
seqfilter in the script, while I am not sure if it functions and it's 
you want.


> I would appreciate it if someone could point me to an example script 
> for this kind of thing. I did not see anything like this in my 
> perusals of the archives or google, please forgive me if this question 
> has been asked before!
> Thanks
> Peter
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Juguang Xiao

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