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

Ashika Umanga Umagiliya aumanga at biggjapan.com
Tue Jun 16 09:41:54 UTC 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 :  http://i43.tinypic.com/e5iu12.png

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 
http://lists.open-bio.org/pipermail/biojava-l/2009-June/006707.html , if 
somehow get all (or fill) all the callbases same as in ACE , I can align 

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.
> Andy
> 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
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l

More information about the Biojava-l mailing list