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A common lisp library for representing and processing biological data such as sequences, genes, proteins, etc...
Common Lisp
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align
data
doc
entrez
examples
io
rucksack
taxonomy
test
.gitignore
COPYRIGHT
README
TODO
annotation.lisp
article.lisp
bio-object.lisp
bio-sequence.lisp
chip.lisp
cl-bio-align.asd
cl-bio-doc.asd
cl-bio-entrez-doc.asd
cl-bio-entrez-test.asd
cl-bio-entrez.asd
cl-bio-rucksack.asd
cl-bio-taxonomy.asd
cl-bio-test.asd
cl-bio.asd
cl-bio.lisp
defpackage.lisp
descriptor.lisp
dictionary.lisp
encoding.lisp
gene.lisp
identifier.lisp
make-dist.sh
range.lisp
scratch.lisp
utilities.lisp

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.
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