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:[EMAIL PROTECTED]
Sent: Mon 6/10/2003 11:51 p.m.
To: [EMAIL PROTECTED]
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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