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

[Muhammad Tariq Pervez]

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