[Biojava-l] Alignment consensus calculation

[mark.schreiber at novartis.com]

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 at sheffield.ac.uk>
Sent by: biojava-l-bounces at lists.open-bio.org
05/18/2006 11:44 PM
Please respond to n.haigh

 
        To:     <biojava-l at lists.open-bio.org>
        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
 
----------------------------------------------------------------------------
------
Dr. Nathan S. Haigh
Bioinformatics PostDoctoral Research Associate
 
Room B2 211                                            Tel: +44 (0)114 22
20112
Department of Animal and Plant Sciences                Mob: +44 (0)7742 
533
569
University of Sheffield                                Fax: +44 (0)114 22
20002
Western Bank                                           Web:
www.bioinf.shef.ac.uk
Sheffield                                             
     www.petraea.shef.ac.uk
S10 2TN                                                
----------------------------------------------------------------------------
------
 


---
avast! Antivirus: Outbound message clean.
Virus Database (VPS): 0620-2, 18/05/2006
Tested on: 18/05/2006 16:44:01
avast! - copyright (c) 1988-2006 ALWIL Software.
http://www.avast.com



_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l