ChipCheck-A Program Predicting Total Hybridization Equilibria for DNA Binding to Small Oligonucleotide Microarrays

Siegmund, Karsten H.; Steiner, Ulrich; Richert, Clemens

ChipCheck-A Program Predicting Total Hybridization Equilibria for DNA Binding to Small Oligonucleotide Microarrays

Dateien

ChipCheck.pdfGröße: 691.32 KBDownloads: 633

Datum

2003

Autor:innen

Siegmund, Karsten H.

Steiner, Ulrich

Richert, Clemens

Open Access-Veröffentlichung

Open Access Green

Sammlungen

Chemie

Publikationstyp

Zeitschriftenartikel

Publikationsstatus

Published

Erschienen in

Journal of chemical information and computer sciences. 2003, 43(6), pp. 2153-2162. ISSN 1549-9596. Available under: doi: 10.1021/ci034049a

Zusammenfassung

Presented here is the program ChipCheck that allows the computation of total hybridization equilibria for hybridization experiments involving small oligonucleotide arrays. The calculation requires the free energies of binding for all pairs of probes and targets as well as total strand concentrations and probe molecule numbers. ChipCheck has been tested computationally on microarrays with up to 100 spots and 42 target strands (4200 binding equilibria). It arrives at solutions through iterations employing the multidimensional Newton method. While currently running in simulation mode only, an extension of the approach to the exhaustive analysis of chip results is being outlined and may be implemented in the future. The output displays the extent of correct and cross hybridization both graphically and numerically. In principle, calculating total hybridization equilibria allows for eliminating noise from DNA chip results and thus an improvement in sensitivity and accuracy.

Fachgebiet (DDC)

540 Chemie

Zitieren

ISO 690

SIEGMUND, Karsten H., Ulrich STEINER, Clemens RICHERT, 2003. ChipCheck-A Program Predicting Total Hybridization Equilibria for DNA Binding to Small Oligonucleotide Microarrays. In: Journal of chemical information and computer sciences. 2003, 43(6), pp. 2153-2162. ISSN 1549-9596. Available under: doi: 10.1021/ci034049a

BibTex

@article{Siegmund2003ChipC-9621,
  year={2003},
  doi={10.1021/ci034049a},
  title={ChipCheck-A Program Predicting Total Hybridization Equilibria for DNA Binding to Small Oligonucleotide Microarrays},
  number={6},
  volume={43},
  issn={1549-9596},
  journal={Journal of chemical information and computer sciences},
  pages={2153--2162},
  author={Siegmund, Karsten H. and Steiner, Ulrich and Richert, Clemens}
}

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Universitätsbibliographie

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