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A common lisp library for representing and processing biological data such as sequences, genes, proteins, etc...
Common Lisp Shell
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========== 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: * FASTA * 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.