[Biojava-dev] traceviewer and phred scores

[Schreiber, Mark]

Hi -

My reccomendation would be to make a class like ABITrace renderer that
uses the Phred Scores to calculate the size of the peaks rather than the
ABIScores.

The other approach would be to align the two. In BioJava you can do a
pairwise alignment using an HMM (I think there is an example in Demos).
I think that the first option is best the ABITrace and the Phred scores
are somewhat disjunct due to the post processing Phred does.

- Mark


> -----Original Message-----
> From: Jun Wan [mailto:jwan at Phylos.com] 
> Sent: Saturday, 15 February 2003 8:32 a.m.
> To: 'biojava-dev at biojava.org'
> Subject: [Biojava-dev] traceviewer and phred scores
> 
> 
> Hi folks,
> I intended to write a sequence traceviewer with phred scores 
> displayed underneath each base calls. The approach would be 
> writing a new renderer that displays phred scores, and add 
> it, along with AbiTraceRenderer, to the MultiLineRenderer, 
> the problem is: the base calls generated by phred program is 
> slighly different from the sequences returned by 
> org.biojava.bio.program.abi.ABITrace.getSequence(),
> including some insertions and deletions at both ends where 
> chromatogram is not as good, how can I align the phred 
> scores/base-calls properly with the chromatogram and 
> sequences from ABITrace.getSequence()? I don't see the 
> alignment functions in biojava-1.3pre1, for Java 1.3. I just 
> started to look at this package, and it was very impressive. 
> But please pardon me if I missed something here. You guys 
> have done a great job. Thanks!
> 
> 
> Jun Wan
> Database Developer and Administrator
> Phylos, Inc.
> 781-862-6400 x359 _______________________________________________
> biojava-dev mailing list
> biojava-dev at biojava.org 
> http://biojava.org/mailman/listinfo/biojava-dev
> 
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