If they are similar enough and you have complete genomes, you may use ClustalW or some other similar MSA. If they have genome rearrangements then you will have to use BLAST as others have noted. ClustalW does not work well when the order of the genes is shifted.
Marty On Wed, Sep 16, 2009 at 8:51 PM, 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 > -- -- Martin Gollery Senior Bioinformatics Scientist Tahoe Informatics www.bioinformaticist.biz www.hiddenmarkovmodels.com _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
