[Biopython-dev] a sequence set object in biopython?

[Giovanni Marco Dall'Olio]

Hi,
I think it could be useful to add a generic SequenceSet object in biopython.
Such an object would represent a generic set of sequences, and could
have some useful methods like .format('fasta') or
.align('alignment_tool').
Is there something similar available already?
I have noticed that the actual Generic.Alignment is very similar to
such an object. However, it would be better to be able to work with a
separated class, because sometimes you want to deal with sequences
that are not aligned.

Some use cases:
- a set of sequences that represents all introns in a particular gene,
on which I want to calculate the conservation of the splicing
regulatory sites.
- all genes sequences in an organisms, which I want to convert in EMBL format
- a set of seqs to be aligned or used as input for other tools
etc..
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