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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 email@example.com