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Re: [Biojava-l] Aligning Chromatogram with Phrap ACE sequences ? Ashika Umanga Umagiliya Tue Jun 16 03:00:47 2009

Hi Andy,

Thank you for the reply.
Earlier problem was I had not applied the compliment in the ChromatoGraph.
Now I could inspect the alignment with the Phrap calls

Please refer :

I have drawn orange underlines from where the two sequences matches.
But I had to hardcode x1 and x2 offset values to make the graphs align with the Phrap basecalls. So as for my question , if somehow get all (or fill) all the callbases same as in ACE , I can align easily.

Best Regards,

Andy Yates wrote:
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 :
image 2 (end of graph):

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

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.
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