Define own alphabet and perform MultipleSequenceAlignment in biopython

Question

[osterland]

I want to do a MultipleSequenceAlignment in biopython but with a self defined Alphabet. The Background is: My sequences are sequences of numeric states and there are up to 5000 states. Thus I need an alphabet with 5000 letters, e.g. '0001', '0042', '4999'. Those sequences are up to 50 states/letters long.

So my main questions are:

• How can I define such an Alphabet?
• How can I use this Alphabet with the MultipleSequenceAlignment?

Alternatively: Is it possible to perform a MultipleSequenceAlignment on Lists/Arrays instead of Sequences?

Thanks for you Time & Help!

[inbar.orr]

Have you had any success here? I am very much interested in your solution.

Answer 1

[Peter]

While the Biopython Alphabet class system could probably mostly handle this, the Seq, SeqRecord and MultipleSequenceAlignment objects all focus on single-letter character representations. You might have some success with the array based MutableSeq object, but I think you would have to write some new subclasses if you really wanted to go down this route.