it is actually possible to find orthologous relationship using the Inparanoid software among 3 organisms.
On Thu, Sep 17, 2009 at 6:25 PM, Dan Bolser <[email protected]> wrote: > 2009/9/17 Nevan King <[email protected]>: >> 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. > > Often the answer to this sort of question is 'there is more than one > way to do it', and the way that you use usually depends on what you > want to see... > > I would suggest something like this: > > 1) blast all genes of organism A against organism B and vice verse > (as described above). > > 2) Pick 'orthologues' using the 'reciprocal best hits' method (i.e. if > gene Ax' and gene Bx'' both find each other as the 'top blast hit' in > the respective organisms gene list, call them an orthologus pair. > > 3) Repeat step 1 and 2, but use organism A and C instead of A and B. > > 4) Pick 'orthologues' when Ax' and Bx'' are an orthologus pair AND Ax' > and Cx''' are an orthologus pair. > > 5) er... do you need to do B vs. C? > > >> Thanks >> >> Nevan. > > Once you get the above blast results (A vs. B, A vs. C, B vs. C and > vice verse) into a database, you will have more than enough data to > play with. You can then define orthologues however you like. > > > That is just one idea to get you going. > > HTH > Dan. > > >> _______________________________________________ >> BBB mailing list >> [email protected] >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
