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Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization

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Publisher
Oxford University Press
Publication Date
Keywords
  • Dna Microarray Measurements Are Susceptible To Error Caused By Non-Specific Hybridization Between A
  • Or Between Two Targets (Bulk-Hybridization)
  • Search Algorithms Such As Blastn Can Quickly Identify Potentially Hybridizing Sequences
  • We Set Out To Improve Blastn Accuracy By Modifying The Substitution Matrix And Gap Penalties
  • We Generated Gene Expression Microarray Data For Samples In Which 1 Or 10% Of The Target Mass Was An
  • We Found That The 10% Spike Induced 2-Fold Intensity Changes In 3% Of The Probes
  • Two-Third Of Which Were Decreases In Intensity Likely Caused By Bulk-Hybridization
  • These Changes Were Correlated With Similarity Between The Spike And Probe Sequences
  • Interestingly
  • Even Very Weak Similarities Tended To Induce A Change In Probe Intensity With The 10% Spike
  • Using This Data
  • We Optimized The Blastn Substitution Matrix To More Accurately Identify Probes Susceptible To Non-Sp
  • Relative To The Default Substitution Matrix
  • The Optimized Matrix Features A Decreased Score For A–T Base Pairs Relative To G–C Base Pairs
  • Resulting In A 5–15% Increase In Area Under The Roc Curve For Identifying Affected Probes
  • This Optimized Matrix May Be Useful In The Design Of Microarray Probes
  • And In Other Blastn-Based Searches For Hybridization Partners

Abstract

Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization - DTU Orbit (20/04/14) Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization - DTU Orbit (20/04/14) Eklund, Aron Charles; Friis, Pia; Wernersson, Rasmus; Szallasi, Zoltan Imre / Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization. In: Nucleic Acids Research, Vol. 38, No. 4, 2010, p. e27. Publication: Research - peer-review › Journal article – Annual report year: 2010

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