[BiO BB] Find common regions in 3 organisms

Martin Gollery marty.gollery at gmail.com
Thu Sep 17 11:46:23 EDT 2009

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.


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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Martin Gollery
Senior Bioinformatics Scientist
Tahoe Informatics

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