MATLAB: Is it possible to customize the sequence alignment function SWALIGN in Bioinformatics Toolbox 3.3 (R2009a)

Question

I am trying to use SWALIGN, to align sequences which use custom alphabets in MATLAB 7.8 (R2009a). I cannot do this, since the function only accepts two default alphabets. I would like to know if there is a way to use custom alphabets with SWALIGN.

Answer 1

The functionality to use custom alphabets is unavailable in Bioinformatics Toolbox 3.3 (R2009a).

As a workaround, you can do a one-to-one mapping between your alphabet and the accepted alphabets. Note that, this will only work if your alphabet has fewer than 26 letters.