[BiO BB] Find common regions in 3 organisms

[Kie Kyon Huang]

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 <dan.bolser at gmail.com> wrote:
> 2009/9/17 Nevan King <nevan.ml at gmail.com>:
>> 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.
>
>
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