Re: Alignment consensus calculation

Hi -

Take a look at the Distribution examples in 
http://biojava.org/wiki/BioJava:Cookbook





"Nathan S. Haigh" <n.haigh@xxxxxxxxxxxxxxx>
Sent by: biojava-l-bounces@xxxxxxxxxxxxxxxxxx
05/19/2006 06:23 PM
Please respond to n.haigh

 
        To:     <mark.schreiber@xxxxxxxxxxxx>
        cc:     biojava-l@xxxxxxxxxxxxxxxxxx
        Subject:        Re: [Biojava-l] Alignment consensus calculation


Sorry for being really thick :o) BUT, how do you get the frequencies of 
the
symbols at each position in the alignment?

I have:
Distribution[] dist = DistributionTools.distOverAlignment(alignment, 
true);

But can figure out how to access the frequencies I need.

Cheers! :o)
Nath

> -----Original Message-----
> From: mark.schreiber@xxxxxxxxxxxx [mailto:mark.schreiber@xxxxxxxxxxxx]
> Sent: 19 May 2006 03:16
> To: n.haigh@xxxxxxxxxxxxxxx
> Cc: biojava-l@xxxxxxxxxxxxxxxxxx
> Subject: Re: [Biojava-l] Alignment consensus calculation
> 
> Hi -
> 
> To get a Distribution[] over an alignment you could use
> DistributionTools.distOverAlignment(a) or one of the other overloaded
> methods.
> 
> To get a consensus you could simply find the most frequent Symbol in 
each
> Distribution. To make a more sophisticated consensus you could have
> thresholds below which you would report an ambiguity.
> 
> eg if:
> 
> a = 0.50
> t = 0.40
> c = 0.0
> g = 1.0
> 
> Your routine would need to decide if the consensus should be 'a' or 'w' 
or
> the IUPAC symbol for [atg] which I cannot remember. You would probably 
use
> some sort of cutoff value. It might be a routine like this:
> 
> public SymbolList consensus(Alignment a, double threshold){
>    ....
> }
> 
> It might be a method that others find useful so please post it back to 
the
> list.
> 
> Hope this helps,
> 
> - Mark
> 
> Mark Schreiber
> Research Investigator (Bioinformatics)
> 
> Novartis Institute for Tropical Diseases (NITD)
> 10 Biopolis Road
> #05-01 Chromos
> Singapore 138670
> www.nitd.novartis.com
> 
> phone +65 6722 2973
> fax  +65 6722 2910
> 
> 
> 
> 
> 
> "Nathan S. Haigh" <n.haigh@xxxxxxxxxxxxxxx>
> Sent by: biojava-l-bounces@xxxxxxxxxxxxxxxxxx
> 05/18/2006 11:44 PM
> Please respond to n.haigh
> 
> 
>         To:     <biojava-l@xxxxxxxxxxxxxxxxxx>
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-l] Alignment consensus calculation
> 
> 
> I was wondering if there were any methods for generating a consensus
> sequence for alignments? Or any suggestions for calculating the 
frequency
> of
> symbols at each position in an alignment.
> 
> I had a look at the DistributionTools after seeing a past e-mail to the
> list
> but couldn't figure if this would do the job as I'm new to Java.
> 
> Thanks
> Nath
> 
> 
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> --
> ------
> Dr. Nathan S. Haigh
> Bioinformatics PostDoctoral Research Associate
> 
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22
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