[BiO BB] Find common regions in 3 organisms

Mike Marchywka marchywka at hotmail.com
Thu Sep 17 10:16:54 EDT 2009

> Date: Thu, 17 Sep 2009 11:52:13 +0530
> From: jyotirusia at gmail.com
> To: bbb at bioinformatics.org
> Subject: Re: [BiO BB] Find common regions in 3 organisms
> Hi
> Nevan
> you can go for multiple sequence alignment for finding common regions in
> more than two sequences..
> try this link
> http://www.ebi.ac.uk/Tools/clustalw2/index.html
> and use clustal W for aligning more than two sequences.
> thanks

The only reason I mentioned this in passing after a long spiel on
the string matching approach was I didn't think it would work in
reasonable time for the initial objective nor find genes that are in different locations etc.
If you just want to align different strains and have a very very fast
computer, it might be possible. If you are looking for orthologues that 
could be anywhere it probably won't work. If you have blast hits 
and want to look at these, then, sure it is a tool. 
Personally I found that making ad hoc or app specific indexes is quite helpful and flexible  and can be very fast if you are just asking "where are these things similar?" Since your index tells you how many entries there are for a given key, you can make some reasonable guess about a given key being an interesting match or a piece of low complexity filler. 
If you start finding things that only occur once in each input genome, those would presumably be most interesting.
If you expect to use the same approach many times, it may be worth the effort. 
> On Thu, Sep 17, 2009 at 9:21 AM, 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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> --
> Regards,
> Jyoti Rusia Gupta
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