[Biojava-l] RNA Secondary Structure

[Schreiber, Mark]

Hi -
 
One way would be to make a Alphabet for the structure based on Symbols for the ((((....)))) characters. You could then make a cross product of that Alphabet and the RNA alphabet and make SymbolLists over that cross product Alphabet. Each Symbol would then have an RNA component and a structure component.
 
I used this approach for Phred quality data (see org.biojava.bio.program.phred package). I would'nt mind helping with this (although I'm away for the next few days), it would make a great few examples for the biojava in Anger site.
 
- Mark
 
 
 

	-----Original Message----- 
	From: Torsten Waldminghaus [mailto:t.waldminghaus at gmx.de] 
	Sent: Mon 6/10/2003 11:51 p.m. 
	To: biojava-l at biojava.org 
	Cc: 
	Subject: [Biojava-l] RNA Secondary Structure
	
	

	Hi all,
	
	I just started to use BioJava and I like it very much - so thank you to all
	Developers because it saves me a lot of work.
	The idea to use a list of objects instead of a string sounds logical to me
	although it needs a while to get used to it.
	Concerning that I have a question:
	I want so save the secondary structure prediction of RNA Sequences together
	with the sequence itself. For that I use an notation of parenthesis and
	periods like this: ((((.....)))) (stands for a hairpinloop)
	So every nucleotide is represented by one point or parenthesis. The question I
	have is if it is clever to declarate all those points and parenthesis as a
	single Feature at a point Location or if there is a better way maybe by
	connecting a SymbolList of that structure whith the sequence or something
	like that.
	I would be gratefull for any comments and wish to have a nice day,
	Torsten
	
	One more thing: What is the difference between the mailgroups biojava-I ans
	biojava-dev?
	
	
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