Optimization of signal-to-noise ratio for efficient microarray probe design

• DOI: 10.1093/bioinformatics/btw451
• Publication Date: 2016-09-01T07:53:39Z
• Authors: Olga V. Matveeva; Yury D. Nechipurenko; Evgeniy Riabenko; Chikako Ragan; Nafisa N. Nazipova; Aleksey Y. Ogurtsov; Svetlana A. Shaba...
• Keywords: Comparative genomic hybridization; Hybridization probe; DNA–DNA hybridization

Target-specific hybridization depends on oligo-probe characteristics that improve specificity and minimize genome-wide cross-hybridization. Interplay between specific cross-hybridization has been insufficiently studied, despite its crucial role in efficient probe design data analysis.In this study, we defined as a ratio oligo target-specific A microarray database, derived from the Genomic Comparison Hybridization (GCH) experiment performed using Affymetrix platform, contains two different types of probes. The first type oligo-probes does not have target genome their signals are alone. second includes oligonucleotides genomic DNA components combined together total signal. comparative analysis oligo-probes, well nucleotide sequences thermodynamic features was database. comparison revealed negatively affected by low stability fully-paired oligo-target duplex, stable self-folding, G-rich content, including GGG motifs, sequence complexity composition symmetry.Filtering out probes with 'negative' significantly increases dramatically decreasing Selected times higher average, compared to were filtered applying suggested cutoff thresholds described parameters. new approach for is our [e-mail] or [e-mail] available at Bioinformatics online.