[Biojava-l] Aligning Chromatogram with Phrap ACE sequences ?

Andy Yates ayates at ebi.ac.uk
Tue Jun 16 09:10:54 UTC 2009

Hi Ashika,

AB1 files will contain a different basecall to one generated by phrap
since (as far as my memory serves me) ABI's platform has a basecaller
built in. This is the one which is coded into the AB1 file & therefore
chromatogram graphic will pick up on that one. However it's very odd
that the Phrap calls are so distant from the trace itself.

I would have hoped that the ACE file would have contained some kind of
called base -> peak position in the chromatogram. There is always the
option of getting phred to output a SCF file which should contain this
information & see what it thinks its doing. SCFs can be parsed by
BioJava so you should be able to push it straight into your program &
let it handle it.


Ashika Umanga Umagiliya wrote:
> Greetings all,
> Please refer to image 1 : http://i40.tinypic.com/11rsk00.png
> image 2 (end of graph):  http://i44.tinypic.com/2vt4iu8.png
> As shown in image (1) , I draw the basecall sequences of AB1 file,by
> parsing the ACE file generated by Phrap.That is ,for upper part I do not
> read AB1 file.Only read values from ACE file.(values under 'RD' tag in
> ACE file.)In the example, two files are 'sampleA-S-R.AB1' and
> 'sampleA-S-F.AB1'.
> For the bottom part- that is to draw Chromatogram, I use Biojavas
> 'ChromatogramGraphic' class.
> I wanted to align these two parts- that is align 'sampleA-S-R.AB1'
> basecall sequence with 'sampleA-S-R.AB1' chromatogram..and so on...(like
> in ChromasPro).
> But I noticed that basecall sequence of 'ChromatogramGraphic' is totally
> different than that of from ACE file.
> Refer to image (2) ; you can see the two sequences generated by same AB1
> file is different in lenght also.
> What could be the problem here? Any suggestions please
> thanks in advance.
> umanga
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