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A common lisp library for representing and processing biological data such as sequences, genes, proteins, etc...
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align export align:alignment-score
data cl-bio 0.0.12
doc resurrect the ability to build the documentation
entrez fix keyword args in entrez-search
examples fix rna-alignment-example package name
io remove the bio-io package. just put everything in bio now.
rucksack various code cleanup items
taxonomy udpate taxonomy download instructions and path.
test remove comment
.gitignore adding .gitignore
COPYRIGHT cl-bio
README cl-bio 1.1.2
TODO cl-bio 0.2.2
annotation.lisp add repeat-region class
article.lisp add comment about origin of the article and article-set classes
bio-object.lisp cl-bio 0.2.0
bio-sequence.lisp only loop (lenth residues) times when setf'ing residues-string
chip.lisp cl-bio 0.2.0
cl-bio-align.asd add alexandria dependency
cl-bio-doc.asd remove cl-bio-doc-html
cl-bio-entrez-doc.asd bump version to 0.2.7. remove bogus asdf-related package.
cl-bio-entrez-test.asd bump version to 0.2.7. remove bogus asdf-related package.
cl-bio-entrez.asd bump version to 0.2.7. remove bogus asdf-related package.
cl-bio-rucksack.asd bump version to 0.2.7. remove bogus asdf-related package.
cl-bio-taxonomy.asd bump version to 0.2.7. remove bogus asdf-related package.
cl-bio-test.asd bump version to 0.2.7. remove bogus asdf-related package.
cl-bio.asd delete make-dist.sh and clean up ASDF system
cl-bio.lisp cl-bio 0.2.0
defpackage.lisp remove the bio-io package. just put everything in bio now.
descriptor.lisp cl-bio 0.2.0
dictionary.lisp dictionary gf docstrings
encoding.lisp * added codon-target, amino-acid and stop-codon classes
gene.lisp Added gene-summary and entrez-gene parsing of gene-summary.
identifier.lisp add ncbi-pmid identifier
range.lisp * add generic functions: get-ncbi-gis, get-ncbi-loci, get-refseq-ids,
scratch.lisp fix typo and remove bio-io prefix
utilities.lisp split-string-into-lines-string -> split-string-into-lines

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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