Cl Bio Save

A common lisp library for representing and processing biological data such as sequences, genes, proteins, etc...

Project README

========== cl-bio Cyrus Harmon, October 2006


Welcome to the cl-bio project. The idea is that this project will serve as a trivial lisp-based analog of the BioPerl project. Simple, light-weight versions of biological objects and methods on these obejcts will be provided.


Initial biological objects:

Sequences: simple implementations of packed 2-bit DNA and RNA sequences (A,C,G,T and A,C,G,U, respectively). Currently there are two kinds of implementation classes for sequences, simple-sequences and adjustable-seqeuences. The adjustable sequences use the flexichain data structure to store the residues of the sequence, which allows for efficient insertion and deletion of residues.

Ranges: directed ranges with a start and an end, as well as double stranded ranges (ds-range) with an additional strand field, with options +plus-strand+, +minus-strand+, +unknown-strand+, and +both-strands+.

Descriptors: Information about sequences.

Identifiers: Subclasses of descriptors that provide a means of naming sequences

File parsers:


  • NCBI Taxonomy Data

  • PDB (Protein Data Bank)

This is wholely incomplete, but contains some infrastructure for parsing PDB files and utility functions for dealing with continued records and what not.

  • Affymetrix CDF files

Again, incomplete, but some of the infrastructure is there.

  • Affymetrix Annotation files


Thanks to Robert Strandh for making the flexichain package. Thanks to the BioPerl group for inspiration.

Open Source Agenda is not affiliated with "Cl Bio" Project. README Source: slyrus/cl-bio
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