[BiO BB] a validation study

Iddo Friedberg idoerg at burnham.org
Mon Dec 6 17:45:51 EST 2004

l x yi wrote:

>I have developed a new method for searching protein
>banks with PSSM (position-specific matrices). To do a
>validation analysis of the method on real protein
>sequences, I need to decide 
>-- a selection of some position-specific matrices for
>major protein domains
>-- a databank of single sequences
>-- a gold standard of which sequences truly belonged
>to which protein domain
>Could anyone suggest some reliable sources of
>references as to how to conduct this validation
>analysis? Any suggestions are appreciated. 
>Do you Yahoo!? 
>Take Yahoo! Mail with you! Get it on your mobile phone. 
>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org

How about looking at the papers which have already used PSSM-based 
searching, and choosing your benchmarks from there?

Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930

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