Hi Bo,
A starting point for formatted output with conservation symbols is already
implemented for pairwise alignments. You can try it out by removing one of the
protein ID's on line 16 of the cookbook code and replacing line 30 with:
System.out.println(profile.toString(Profile.StringFormat.CLUSTALW));
The code that would need updating for multiple alignments is in
SimpleProfile.printConservation and around the call to it in the toString helper
method.
-Mark
On 2/24/2011 2:06 AM, Andreas Prlic wrote:
Hi Bo Li,
The printing method currently does not add those characters to the
display of the aligned sequences. If you need it you would have to
patch the printing method...
Andreas
On Tue, Feb 22, 2011 at 11:16 PM, Bo Li<[email protected]> wrote:
Hi,
Sorry for the bothering. I tried the MSA feature by following the link:
http://www.biojava.org/wiki/BioJava:CookBook3:MSA
However, I can't see the symbols like ".", ":", and "*" like I can see from
the output ClustalW.
So is there a way for users to obtain such information in the output from
MSA?
Thanks,
Bo Li
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