[BiO BB] Find common regions in 3 organisms

Nevan King nevan.ml at gmail.com
Wed Sep 16 23:51:15 EDT 2009


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.



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