method getProgressiveAlignment in biojava

Question

[ewa_kania-15]

I have problems with using method I biojava in class alignments: getProgressiveAlignment(GuideTree<S,C> tree, Alignments.ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix). I don't know what is Alignments.ProfileProfileAlignerType type and how to use it.

• GuideTree: http://www.biojava.org/docs/api/org/biojava3/alignment/GuideTree.html
• Alignments.ProfileProfileAlignerType: http://www.biojava.org/docs/api/org/biojava3/alignment/Alignments.ProfileProfileAlignerType.html
• GapPenalty: http://www.biojava.org/docs/api/org/biojava3/alignment/template/GapPenalty.html
• SubstitutionMatrix: http://www.biojava.org/docs/api/org/biojava3/alignment/template/SubstitutionMatrix.html

Answer 1

[mikhail.shugay]

This is an enum to specify the algorithm used for the alignment. Using global and local alignment depends on the expected structure of alignment: large divergent sequences spanned by short highly similar regions, etc. You should start with some general reading: http://en.wikipedia.org/wiki/Sequence_alignment