[BiO BB] Find common regions in 3 organisms

[Harry Mangalam]

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.
>
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