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:

  • 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.

Open Source Agenda is not affiliated with "Cl Bio" Project. README Source: slyrus/cl-bio
Stars
28
Open Issues
0
Last Commit
3 years ago
Repository
Tags

Open Source Agenda Badge

Open Source Agenda Rating