[Biojava-l] Biojava in Artemis

[Schreiber, Mark]

Hi -
 
David Huen (I think) checked in some stuff for codon usage into biojava-live. Called CodonPref and CodonPrefFilter (and possibly others).
 
Not sure how they are used yet. David?
 
- mark
 

	-----Original Message----- 
	From: Thomas Down [mailto:thomas at derkholm.net] 
	Sent: Tue 26/08/2003 9:04 p.m. 
	To: Derek Gatherer 
	Cc: biojava-l at biojava.org 
	Subject: Re: [Biojava-l] Biojava in Artemis
	
	

	Once upon a time, Derek Gatherer wrote:
	> Hi
	>
	> I have a couple of questions regarding codon bias measurements.
	>
	> 1) Is there a codon usage object in Biojava?
	> 2) How easy would it be to integrate it into Artemis (to add things to the
	> Graph menu)?
	>
	> I've seen references to
	> CrossProductAlphabet codonAlphabet = AlphabetManager
	>
	> in the archive, so I think I can manage to generate a codon usage table,
	> and compute codon bias statistics from that, but I was wondering if
	> something more complete has already been written.
	>
	> I have been using TreeMaps to make codon usage tables within Artemis
	> classes, but they seem to be very slow, eg:
	> Collator co = Collator.getInstance();
	> TreeMap codonUsageTable = new TreeMap(co);
	>
	> and then accessing them using .put() and .get() TreeMap methods.  But the
	> performance is poor compared to the Artemis classes that just read single
	> chars, eg GCFrameAlgorithm.
	
	BioJava applications generally represent codons as symbols over
	the alphabet DNA * DNA * DNA (or RNA * RNA * RNA).  There are
	Distribution objects (in the org.biojava.bio.dist package) that
	are reasonably fast and could be used to calculate and store
	a probability distribution over the codon alphabet.
	
	I don't know of a single example program which does exactly
	what you want, but most of the pieces are in the tutorial.
	Take a look at:
	
	    http://www.biojava.org/docs/bj_in_anger/index.htm
	
	with particular reference to the sections headed `Alphabets
	and Symbols' and `Counts and Distributions'.
	
	Hope this helps,
	
	   Thomas.
	_______________________________________________
	Biojava-l mailing list  -  Biojava-l at biojava.org
	http://biojava.org/mailman/listinfo/biojava-l
	


=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================