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

[Ashika Umanga Umagiliya]

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