[Biojava-dev] No. of gaps in aligned sequences

Muhammad Tariq Pervez tariq_cp at hotmail.com
Wed Jul 6 11:37:05 UTC 2011



Hi, Dear all,
I am working on the development of MSA application using BioJava. I want to make clear a thing. It is that when two or more protein sequences are aligned the '-' is shown more times in an aligned sequence than the gaps display by the method of alSeq.getNumGaps(). 'alSeq' is an aligned sequence. For example, if there are actual 50 '-' in an aligned sequence but the method shows it only 30. What is the difference between these two results.

Best Regards


Tariq, Phd Scholar
 		 	   		  


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