[Biojava-l] Any ORF Finder available ?

[mark.schreiber at novartis.com]

Hi -

A quick and dirty way is to make a six frame translation 
(http://biojava.org/wiki/BioJava:Cookbook:Translation:SixFrames).

Probably a better way is to scan in six frames (using a 
WindowedSymbolList) looking for a start codon and then look for the 
appropriate stop codon. You will want to define the start and stop codons 
as Symbols from the codon (DNAxDNAxDNA) alphabet. You can do this as 
follows:

FiniteAlphabet codonAlpha = DNATools.getCodonAlphabet();

//make a ambiguity symbol for ATG, GTG and TTG codons

//first make the A or G or T ambiguity BasisSymbol
Set syms = new HashSet();
syms.add(DNATools.a()); syms.add(DNATools.t()); syms.add(DNATools.g());
Symbol amb = DNATools.getDNA().getAmbiguity(syms) ;

//now make the [A|G|T] TG codon
List l = new ArrayList();
l.add(amb); l.add(DNATools.t()); l.add(DNATools.g());
Symbol startCodon = codonAlpha.getSymbol(l);

//You would construct the stop codons in a similar manner although you 
probably can't merge them all into one.

The above example shows how you can use a single symbol to represent all 3 
common bacterial start codons. You could also make all 3 seperatly and 
test them individually.

- Mark
 

Mark Schreiber
Research Investigator (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
www.dengueinfo.org

phone +65 6722 2973
fax  +65 6722 2910





Benoit VARVENNE <varvenne at genoway.com>
Sent by: biojava-l-bounces at lists.open-bio.org
11/21/2006 12:19 AM

 
        To:     biojava-l <biojava-l at lists.open-bio.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Any ORF Finder available ?


Hello,

I'm a working on a biojava project and i'm searching for a way to include 
an
ORF Finder in my code. The aim is to find ORFs on cDNA sequences (or 
partial
ORFs on ESTs ones) 

Anyone can help me ?
Is there a module with biojava to do so ? Do you know any free-to-dowload
software (source code or compiled one) ?

Thanks,
Regards 

Benoît.


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