[Biojava-dev] Alignment SmithWaterman and NW

[Sylvain Foisy]

Hi,

This might be a stupid question but have you tried these same sequences
using EMBOSS' water and needle with the same parameters? If you get the same
output, it might be the sequences themselves.

Best regards

Sylvain

On 08/11/06 17:27, "Emig, Robin" <Robin.Emig at pioneer.com> wrote:

> I just test out the alignment procedure in biojava and found a
> possible issue. When aligning two sequences, I get an alignment which
> contains gaps at the same position in both sequences. This seems strange
> to me, can it be correct?


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Sylvain Foisy, Ph. D.
Consultant
Diploide.net - TI pour la vie / IT for Life

Courriel: sylvain.foisy at diploide.net

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