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

[Andreas Prlic]

Hi Tariq,

Can you send us the sample code / DB accession IDs so we can try to
reproduce this?

Andreas

On Wed, Jul 6, 2011 at 4:37 AM, Muhammad Tariq Pervez
<tariq_cp at hotmail.com> wrote:
>
>
> 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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