title: keeSeek: searching distant non-existing words in genomes for PCR-based applications.
abstract: The search for short words that are absent in the genome of one or more organisms (neverwords, also known as nullomers) is attracting growing interest because of the impact they may have in recent molecular biology applications. keeSeek is able to find absent sequences with primer-like features, which can be used as unique labels for exogenously inserted DNA fragments to recover their exact position into the genome using PCR techniques. The main differences with respect to previously developed tools for neverwords generation are (i) calculation of the distance from the reference genome, in terms of number of mismatches, and selection of the most distant sequences that will have a low probability to anneal unspecifically; (ii) application of a series of filters to discard candidates not suitable to be used as PCR primers. KeeSeek has been implemented in C++ and CUDA (Compute Unified Device Architecture) to work in a General-Purpose Computing on Graphics Processing Units (GPGPU) environment.
  
  
  METHODS
  Freely available under the Q Public License at http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=keeseek.
authors.affiliation: Department of Molecular Medicine, University of Padova, Padova, I-35131, Italy and Department of Computational Biology, Edmund Mach Foundation, S. Michele All'Adige, I-38010 (TN), Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Falda
authors.affiliation: Department of Molecular Medicine, University of Padova, Padova, I-35131, Italy and Department of Computational Biology, Edmund Mach Foundation, S. Michele All'Adige, I-38010 (TN), Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Fontana
authors.affiliation: Department of Molecular Medicine, University of Padova, Padova, I-35131, Italy and Department of Computational Biology, Edmund Mach Foundation, S. Michele All'Adige, I-38010 (TN), Italy.
authors.forename: Luisa
authors.initials: L
authors.lastname: Barzon
authors.affiliation: Department of Molecular Medicine, University of Padova, Padova, I-35131, Italy and Department of Computational Biology, Edmund Mach Foundation, S. Michele All'Adige, I-38010 (TN), Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Toppo
authors.affiliation: Department of Molecular Medicine, University of Padova, Padova, I-35131, Italy and Department of Computational Biology, Edmund Mach Foundation, S. Michele All'Adige, I-38010 (TN), Italy.
authors.forename: Enrico
authors.initials: E
authors.lastname: Lavezzo
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D057225:Data Mining; D023281:Genomics / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000235:genetics; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D017931:DNA Primers