[BiO BB] Find common regions in 3 organisms

Lijo lijo.skb at gmail.com
Thu Sep 17 02:11:23 EDT 2009

Neaven, I don't know you are talking about basic multiple alignment. if so,
you have plenty of tools to try with.
And if your input space is big you may download static version for clusters
and try.

On Wed, Sep 16, 2009 at 8:51 PM, Nevan King <nevan.ml at gmail.com> 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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