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Code for computing minimal reverse-complementary-covering DNA oligomer libraries

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README
Computing MRCC libraries and related types of DNA oligomer libraries

SJ Riesenfeld
Feb 2012

An MRCC library is a DNA oligomer library that contains exactly one
copy of exactly one representative for each k-bp sequence (k-mer) and
its reverse complement. For double-stranded DNA experiments, it can be
useful for a library to have this property. For even values of k
greater than 2, however, it is not possible to output a single
sequence with this property, i.e., there is no analog for a de Bruijn
sequence in the context where each k-mer and its reverse complement
are restricted to a single representative. It is possible to compute a
set of sequences with this property, for set sizes that are much
smaller than the number of k-mers (or reverse-complementary k-mer
pairs). This code was developed to do that.

The main program for computing such a library is
"design_oligomers.pl". Basic documentation is accessible by typing
"design_oligomers.pl -h" at the prompt. To see an example, you can
type:

perl design_oligomers.pl 

at the command prompt, and the program will run with the default
settings to create a library of 208 oligomers, each 15bp in length,
for k=6, in an output file called "oligomer_library_design.txt". 

An example of this output file is in
"example_oligomer_lib_design.txt". There are 4,096 6-bp sequences, and
each one *or* its reverse complement (but not both) appears exactly
once in the output library of sequences.

It is possible to use this software to produce a modified version of
the library that takes into account the flanking sequences for a given
experimental application. The flanking sequences introduce repetitions
in k-mers across the junctions between oligomers and flanking
sequence.The code attempts to minimize these reptitions and exploit
them to reduce oligomer library size. However the output is not a true
MRCC library, and flanking sequences are required to ensure coverage
of all k-mers.

Please see the program and module files for additional documentation.
Questions? Contact sriesenfeld@gmail.com
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