Based on the question & follow-ups, it sounds like you want is a complete genome similarity comparison. Have you looked at Vista (no relation to MS)?
http://genome.lbl.gov/vista/index.shtml That's what it does (among an increasing list of other things)... hjm On Wednesday 16 September 2009 20:51:15 Nevan King wrote: > Hi, > > This question has probably been asked, but I'm not sure what search > terms to use to find answers. This is a question from one of the > researchers in my lab. > > I want to find common regions of sequences in 3 organisms. The first > organism (P. gingivalis) has been fully sequenced and described. It > has around 2000 genes. The other two are similar to P. gingivalis. > > I've set up all three organisms in Blast, but comparing the genes one > by one would be a big task. What's the best way to automate this? I > understand that you can enter a list of fastas into blast and it will > compare each one to all the genes in its database. Is there a way to > do this with 3 organisms? Is Blast the best tool to use for this job? > > Sorry if this is short on details, I don't fully understand the topic. > > Thanks > > Nevan. > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb -- Harry Mangalam - Research Computing, NACS, Rm 225 MSTB, UC Irvine [ZOT 2225] / 92697 949 824-0084(o), 949 285-4487(c) MSTB=Bldg 415 (G-5 on <http://today.uci.edu/pdf/UCI_09_map_campus.pdf> --- It is better to be roughly right than precisely wrong. Keynes _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
