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

branch: master
Octocat-spinner-32 align alignment improvements -- special variables for gap costs, etc... January 24, 2011
Octocat-spinner-32 data cl-bio 0.0.12 March 17, 2008
Octocat-spinner-32 doc resurrect the ability to build the documentation January 24, 2011
Octocat-spinner-32 entrez remove the bio-io package. just put everything in bio now. October 09, 2010
Octocat-spinner-32 examples print-alignment -> alignment-results October 02, 2008
Octocat-spinner-32 io remove the bio-io package. just put everything in bio now. October 09, 2010
Octocat-spinner-32 rucksack various code cleanup items May 23, 2010
Octocat-spinner-32 taxonomy udpate taxonomy download instructions and path. June 25, 2010
Octocat-spinner-32 test various code cleanup items May 23, 2010
Octocat-spinner-32 .gitignore adding .gitignore April 20, 2008
Octocat-spinner-32 COPYRIGHT cl-bio October 26, 2006
Octocat-spinner-32 README cl-bio 1.1.2 November 12, 2007
Octocat-spinner-32 TODO cl-bio 0.2.2 March 20, 2008
Octocat-spinner-32 annotation.lisp Add cds class March 28, 2008
Octocat-spinner-32 article.lisp add comment about origin of the article and article-set classes May 23, 2010
Octocat-spinner-32 bio-object.lisp cl-bio 0.2.0 March 17, 2008
Octocat-spinner-32 bio-sequence.lisp only loop (lenth residues) times when setf'ing residues-string January 24, 2011
Octocat-spinner-32 chip.lisp cl-bio 0.2.0 March 17, 2008
Octocat-spinner-32 cl-bio-align.asd add alexandria dependency January 07, 2011
Octocat-spinner-32 cl-bio-doc.asd update to work with new smarkup January 24, 2011
Octocat-spinner-32 cl-bio-entrez-doc.asd bump version to 0.2.7. remove bogus asdf-related package. May 23, 2010
Octocat-spinner-32 cl-bio-entrez-test.asd bump version to 0.2.7. remove bogus asdf-related package. May 23, 2010
Octocat-spinner-32 cl-bio-entrez.asd bump version to 0.2.7. remove bogus asdf-related package. May 23, 2010
Octocat-spinner-32 cl-bio-rucksack.asd bump version to 0.2.7. remove bogus asdf-related package. May 23, 2010
Octocat-spinner-32 cl-bio-taxonomy.asd bump version to 0.2.7. remove bogus asdf-related package. May 23, 2010
Octocat-spinner-32 cl-bio-test.asd bump version to 0.2.7. remove bogus asdf-related package. May 23, 2010
Octocat-spinner-32 cl-bio.asd remove bogus file reference October 09, 2010
Octocat-spinner-32 cl-bio.lisp cl-bio 0.2.0 March 17, 2008
Octocat-spinner-32 defpackage.lisp remove the bio-io package. just put everything in bio now. October 09, 2010
Octocat-spinner-32 descriptor.lisp cl-bio 0.2.0 March 17, 2008
Octocat-spinner-32 dictionary.lisp dictionary gf docstrings April 20, 2008
Octocat-spinner-32 encoding.lisp * added codon-target, amino-acid and stop-codon classes March 25, 2008
Octocat-spinner-32 gene.lisp Added gene-summary and entrez-gene parsing of gene-summary. June 23, 2010
Octocat-spinner-32 identifier.lisp add ncbi-pmid identifier July 26, 2009
Octocat-spinner-32 make-dist.sh use (dirname "$0") so that running make-dist.sh from another director… April 19, 2008
Octocat-spinner-32 range.lisp * add generic functions: get-ncbi-gis, get-ncbi-loci, get-refseq-ids, March 29, 2008
Octocat-spinner-32 scratch.lisp fix typo and remove bio-io prefix October 09, 2010
Octocat-spinner-32 utilities.lisp split-string-into-lines-string -> split-string-into-lines July 03, 2008
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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