Hi Nevan you can go for multiple sequence alignment for finding common regions in more than two sequences..
try this link http://www.ebi.ac.uk/Tools/clustalw2/index.html and use clustal W for aligning more than two sequences. thanks On Thu, Sep 17, 2009 at 9:21 AM, Nevan King <[email protected]> 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 > -- Regards, Jyoti Rusia Gupta The greatest gift you can give to someone is your time because when you give someone your time, you have given them a portion of your life that you'll never get back" . _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
