[BiO BB] looking for interactive motif/conserved things or rule site

Mike Marchywka marchywka at hotmail.com
Tue Jun 2 13:59:59 EDT 2009




Hi,

I found this site a few years ago,

http://www.expasy.ch/prosite/prorule.html

and downloaded their rules to generate
some tools such as these,

http://www.spottext.com/marchywka/annotaters/docs.html

I've found it useful to be able to harvest my own rules from
literature and wrote a program to convert XML entries including
all the source information into "one-liners"
that describe each rule as a regular expression along with a terse name and citation.
Then, I got the bright idea that I could find many motifs using
ncbi's eutils facilities and some scripts. And, indeed this was possible,
as I was able to extract perhaps 800 rules but I needed to manually
edit them. In any case, I was wondering who else
used the prosite facilities or things like it
and if there were generated or author deposited pattern libraries
somewhere?

They do let you enter your own sequence here,

http://www.expasy.org/tools/scanprosite/

but not sure if there is any thing more comprehensive for
user entered patterns that may be questionable or wrong
or just entered for discussion( like the wiki talk pages).

As an example, I was reading this article,

http://www.jbc.org/cgi/content/full/282/48/34929

and wanted to generate rules from the peptides and maybe put
them into some kind of public data file  maybe with
a discussion page or allow others to curate like a wiki pattern library.

Thoughts or comments on existing facilities that may accomplish these
results ?

Thanks.



Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165
415-264-8477 (w)<- use this
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only
marchywka at hotmail.com
Note: If I am asking for free stuff, I normally use for hobby/non-profit
information but may use in investment forums, public and private.
Please indicate any concerns if applicable.
Note:  hotmail is getting cumbersom, try also marchywka at yahoo.com




_________________________________________________________________
Windows Live™: Keep your life in sync. 
http://windowslive.com/explore?ocid=TXT_TAGLM_WL_BR_life_in_synch_062009



More information about the BBB mailing list