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CANADA 

the Computer Aided Nucleic Acid Design pAckage

CANADA is a collection of tools not only for designing nucleic acid sequences with certain properties,
but also for analyzing and handling them.

The design of nucleic acid sequences is necessary for a wide range of applications, most of which belong
to the fields of DNA-Computing or DNA-based nanotechnology. The most important requirement for
nucleic acid molecules is specific hybridization, i.e. avoidance of any unintended and thus undesired binding
between strands. Furthermore, a high and homogeneous hybridization efficiency of all oligonucleotides and
their intended binding partner is desirable. And, depending on the application, additional restrictions, e.g.
on the molecules' melting temperature, or the specification of fixed subsequences etc., may be necessary.
This multitude of different requirements is joined by the huge search space of nucleic acid sequences,
containing 4n different sequences of length n, and if you regard sets of sequences, combinatorics makes
things even worse. Thus, the aid of computer programs is indispensable. The design tools in CANADA
have been developed to enable the user to find sequences that meet all desired requirements and restrictions.
The other tools, DNA handling ones and others, were developed when necessary during the research on DNA
sequence design, and may be useful to people working with DNA.

CANADA is written in C++. For the time being, all binaries are for the Windows command line. Future plans
include compiling Linux binaries, publishing the source code of at least some of the tools and the DeLaNA parser
with the object classes, polishing and extending the tools, adding some more small tools, and maybe even a GUI or two.

The current version of CANADA is 2.0. This version of the package contains the following tools:

Tool Version Short description
design tools
dsg 2.01 DNA sequence generator
dsc 3.09 DNA sequence compiler
DNA tools
align 1.0 global alignment & duplex stability
clean_out 1.0 removes non-base characters
complement 1.0 puts out Watson-Crick complements
duplex2hairpin 1.0 links two sequences of a duplex to a hairpin loop
gc 1.0 calculates absolute and relative GC content
nb_unique 1.03 searches for non-unique subsequences
rand_seqs 1.01 generates random sequences
reverse 1.0 puts out reverse sequences
seq_dist 1.01 calculates distance between sequence pairs
seq_dist2 1.01 as seq_dist, but for all possible pairs
thermo 1.01 calculates thermodynamic properties such as melting temperature or free energy
other tools
corr_coeff 1.0 calculates linear correlation coefficients
rank_corr 1.0 calculates Spearman rank correlation coefficients

Download

You can follow the links in the above table to get more information on each tool and to download them seperately.
This manual explains how to use these tools (pdf, 400 KB).
Some example input files for quickly testing the tools.
And the complete package, containing the tools, the manual, and the example files (zip, 2.3 MB).

Installation

It is rather easy to install CANADA on your computer: Simply unpack the zip file in any directory that is convenient
for you. In order to use the tools independend on what directory you are currently working in, you might want to add
the path to CANADA's bin directory to your system's path variable. Just click on the Start button, open the Control
Panel (in Settings), open the System dialog, choose the Advanced tab, click on the Environment Variables button,
select PATH, click on the Edit button, add a semicolon and the full path of the bin directory, click OK, click OK again.
Already opened command-line windows may not recognize this change (check with the path command), but freshly
opened command shells should know the new path.

Bugreports, Questions, etc.

If you discover a bug, have a question, want to suggest additional features, or have any praise or complaints, please
send an email to udo.feldkamp (at) uni-dortmund.de.

Old Stuff

Since the current version of the DNA Sequence Generator does not have a GUI, you can download version 1.01b,
which still has one.

And there is also an old version (2.0) of the DNA Sequence Compiler, with GUI, but only capable of turning
regular grammars into base sequences for linear self-assembly.

last modification: Apr/17/2009

  
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