title: Flexible and efficient genome tiling design with penalized uniqueness score.
abstract: BACKGROUND
  As a powerful tool in whole genome analysis, tiling array has been widely used in the answering of many genomic questions. Now it could also serve as a capture device for the library preparation in the popular high throughput sequencing experiments. Thus, a flexible and efficient tiling array design approach is still needed and could assist in various types and scales of transcriptomic experiment.
  
  
  RESULTS
  In this paper, we address issues and challenges in designing probes suitable for tiling array applications and targeted sequencing. In particular, we define the penalized uniqueness score, which serves as a controlling criterion to eliminate potential cross-hybridization, and a flexible tiling array design pipeline. Unlike BLAST or simple suffix array based methods, computing and using our uniqueness measurement can be more efficient for large scale design and require less memory. The parameters provided could assist in various types of genomic tiling task. In addition, using both commercial array data and experiment data we show, unlike previously claimed, that palindromic sequence exhibiting relatively lower uniqueness.
  
  
  CONCLUSIONS
  Our proposed penalized uniqueness score could serve as a better indicator for cross hybridization with higher sensitivity and specificity, giving more control of expected array quality. The flexible tiling design algorithm incorporating the penalized uniqueness score was shown to give higher coverage and resolution. The package to calculate the penalized uniqueness score and the described probe selection algorithm are implemented as a Perl program, which is freely available at http://www1.fbn-dummerstorf.de/en/forschung/fbs/fb3/paper/2012-yang-1/OTAD.v1.1.tar.gz.
authors.affiliation: Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
authors.forename: Yang
authors.initials: Y
authors.lastname: Du
authors.forename: Eduard
authors.initials: E
authors.lastname: Murani
authors.forename: Siriluck
authors.initials: S
authors.lastname: Ponsuksili
authors.forename: Klaus
authors.initials: K
authors.lastname: Wimmers
mesh_terms: D000465:Algorithms; D000818:Animals; D015342:DNA Probes / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data*
chemical_list: D015342:DNA Probes