[BiO BB] Find common regions in 3 organisms

Mike Marchywka marchywka at hotmail.com
Fri Sep 18 20:16:23 EDT 2009

> Date: Thu, 17 Sep 2009 08:46:23 -0700
> From: marty.gollery at gmail.com
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] Find common regions in 3 organisms
> 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.

It works fine for what it is supposed to do - multi sequence alignment. 
These things don't know a lot about likely operations that have been performed to generate one set of features from another source.
If you did this with text and wanted to diff versions of a file that may be fine when files are nominally similar. If you are trying to find similar sentences or paragraphs in texts with no assumed apriori similarity, you can eeither do some kind of NxM exhaustive search or 
build and use various indexes with lower order algorithms. I guess
I'd be curious if there are even "general purpose" string indexers
around that let you operate on the indicies etc. 
> Marty
> On Wed, Sep 16, 2009 at 8:51 PM, 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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> --
> --
> Martin Gollery
> Senior Bioinformatics Scientist
> Tahoe Informatics
> www.bioinformaticist.biz
> www.hiddenmarkovmodels.com
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