Author:

Keywords:

nearest-neighbor model, thermodynamic parameters, gene-expression, dna microarrays, hybridization, behavior, arrays, adsorption, duplexes, Science & Technology, Life Sciences & Biomedicine, Biochemical Research Methods, Biotechnology & Applied Microbiology, Mathematical & Computational Biology, Biochemistry & Molecular Biology, NEAREST-NEIGHBOR MODEL, THERMODYNAMIC PARAMETERS, GENE-EXPRESSION, DNA MICROARRAYS, HYBRIDIZATION, BEHAVIOR, ARRAYS, ADSORPTION, DUPLEXES, Algorithms, Databases, Genetic, Gene Expression Profiling, Microarray Analysis, Oligonucleotide Array Sequence Analysis, RNA, Thermodynamics, 01 Mathematical Sciences, 06 Biological Sciences, 08 Information and Computing Sciences, Bioinformatics, 31 Biological sciences, 46 Information and computing sciences, 49 Mathematical sciences

Abstract:

Background: An algorithm for the analysis of Affymetrix Genechips is presented. This algorithm, referred to as the Inverse Langmuir Method (ILM), estimates the binding of transcripts to complementary probes using DNA/RNA hybridization free energies, and the hybridization between partially complementary transcripts in solution using RNA/RNA free energies. The balance between these two competing reactions allows for the translation of background-subtracted intensities into transcript concentrations.