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1000 Titel
  • Flexible and efficient genome tiling design with penalized uniqueness score
1000 Autor/in
  1. Murani, Eduard |
  2. Ponsuksili, Siriluck |
  3. Du, Yang |
  4. Wimmers, Klaus |
1000 Erscheinungsjahr 2012
1000 Art der Datei
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2012-12-05
1000 Erschienen in
1000 Quellenangabe
  • 13: 323
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2012
1000 Lizenz
1000 Verlagsversion
  • https://doi.org/10.1186/1471-2105-13-323 |
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583072/ |
1000 Ergänzendes Material
  • https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-323#Declarations |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • 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.
1000 Sacherschließung
lokal Probe design
lokal Penalized uniqueness score
lokal Tiling array
lokal Targeted sequencing
1000 Fachgruppe
  1. Biologie |
  2. Agrarwissenschaften |
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://frl.publisso.de/adhoc/creator/TXVyYW5pLCBFZHVhcmQ=|https://frl.publisso.de/adhoc/creator/UG9uc3Vrc2lsaSwgU2lyaWx1Y2s=|http://orcid.org/0000-0002-5707-513X|http://orcid.org/0000-0002-9523-6790
1000 Förderer
  1. German Research Foundation (DFG) |
1000 Fördernummer
  1. Wi 1754/14
1000 Förderprogramm
  1. -
1000 Dateien
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer German Research Foundation (DFG) |
    1000 Förderprogramm -
    1000 Fördernummer Wi 1754/14
1000 Objektart article
1000 Beschrieben durch
1000 @id frl:6404638.rdf
1000 Erstellt am 2017-09-25T10:48:54.776+0200
1000 Erstellt von 218
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1000 Bearbeitet von 218
1000 Zuletzt bearbeitet Wed May 16 12:25:11 CEST 2018
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1000 Vgl. frl:6404638
1000 Oai Id
  1. oai:frl.publisso.de:frl:6404638 |
1000 Sichtbarkeit Metadaten public
1000 Sichtbarkeit Daten public
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