Introduction

Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths. EvOligo combines two modules. The first module performs oligonucleotide design, and the second module performs oligonucleotide grouping. The software applies a nearest-neighbor model of nucleic acid interactions coupled with a parallel evolutionary algorithm to construct individual oligonucleotides, and to group the molecules that are characterized by the weakest possible cross-interactions. To provide optimal solutions, the evolutionary algorithm sorts oligonucleotides into sets, preserves preselected parts of the oligonucleotides, and shapes their remaining parts. In addition, the oligonucleotide sets can be designed and grouped based on their melting temperatures. For the user's convenience, EvOligo is provided with a user-friendly graphical interface. EvOligo was used to design individual oligonucleotides, oligonucleotide pairs, and groups of oligonucleotide pairs that are characterized by the following parameters: (1) weaker cross-interactions between the non-complementary oligonucleotides and (2) more uniform ranges of the oligonucleotide pair melting temperatures than other available software products. In addition, in contrast to other grouping algorithms, EvOligo offers time-efficient sorting of paired and unpaired oligonucleotides based on various parameters defined by the user.

Publications

  1. EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments.
    Cite this
    Milewski MC, Kamel K, Kurzynska-Kokorniak A, Chmielewski MK, Figlerowicz M, 2017-03-01 - Journal of computational biology : a journal of computational molecular cell biology

Credits

  1. Marek C Milewski
    Developer

    1 Institute of Bioorganic Chemistry PAS, Poznan

  2. Karol Kamel
    Developer

    1 Institute of Bioorganic Chemistry PAS, Poznan

  3. Anna Kurzynska-Kokorniak
    Developer

    1 Institute of Bioorganic Chemistry PAS, Poznan

  4. Marcin K Chmielewski
    Developer

    1 Institute of Bioorganic Chemistry PAS, Poznan

  5. Marek Figlerowicz
    Investigator

    2 Institute of Computing Science, Poznan University of Technology

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Summary
AccessionBT006453
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++, Perl
User InterfaceTerminal Command Line
Download Count0
Submitted ByMarek Figlerowicz