Hello,

When I found out about cl-bio a few days ago, I was thrilled to find someone else working on a general common lisp bio package. I started a similar effort some time ago, named CL Computational Biology[1]. It's not in my interest to duplicate any functionality, which is why I'd like to merge the two code bases.

My main suggestion is to merge the bio-sequence implementations. During the implementation of CLCB bio-sequences, we focused on the intuitive handling of sub-intervals. The concept applied here is to regard bio-sequences as discrete intervals. That way, other sequences and features can simply be mapped upon their respective 'supersequence', keeping information of e.g. where an amino acid 'came from'. This also allows for set theoretic handling of bio-sequences. The concept is a modification of the modeling used by the Ensembl project[2].

Disregarding your opinion towards the proposed merge, I'd be delighted to help building a community driven Bio project in eather case.

Best, Albert

[1] No website yet, but some docs in the svn repository: svn co http://clcb.svn.sf.net/svnroot/clcb/trunk clcb

[2] http://www.ensembl.org/info/using/api/core/index.html