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 [email protected] 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 [email protected] _________________________________________________________________ Windows Live™: Keep your life in sync. http://windowslive.com/explore?ocid=TXT_TAGLM_WL_BR_life_in_synch_062009 _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
