Proceedings ArticleDOI
Classification method for microarray probe selection using sequence, thermodynamics and secondary structure parameters
Lalit Gupta,Sanjay Kumar,Randeep Singh,Rafi Shaik,Nevenka Dimitrova,Aparna Gorthi,B. Lakshmi,Deepa Pai,Sitharthan Kamalakaran,Xiaoyue Zhao,Michael Wigler +10 more
- pp 1-5
Reads0
Chats0
TLDR
This paper validate the importance of various features currently used for designing an oligonucleotide probe, and a classification methodology is presented that can be used to predict the hybridization quality of a probe.Abstract:
Probe design is the most important step for any microarray based assay. Accurate and efficient probe design and selection for the target sequence is critical in generating reliable and useful results. Several different approaches for probe design are reported in literature and an increasing number of bioinformatics tools are available for the same. However, based on the reported low accuracy, determining the hybridization efficiency of the probes is still a big computational challenge. Present study deals with the extraction of various novel features related to sequence composition, thermodynamics and secondary structure that may be essential for designing good probes. A feature selection method has been used to assess the relative importance of all these features. In this paper, we validate the importance of various features currently used for designing an oligonucleotide probe. Finally, a classification methodology is presented that can be used to predict the hybridization quality of a probe.read more
References
More filters
Journal ArticleDOI
Predicting DNA duplex stability from the base sequence.
TL;DR: This work reports the complete thermodynamic library of all 10 Watson-Crick DNA nearest-neighbor interactions and shows how these thermodynamic data can be used to calculate the stability and predict the temperature-dependent behavior of any DNA duplex structure from knowledge of its base sequence.
Journal ArticleDOI
Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability†
TL;DR: Improved parameters were derived for the prediction of oligonucleotides dissolved in 1 M NaC1 to suggest that both sequence and base composition are important determinants of DNA duplex stability.
Journal ArticleDOI
Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes.
TL;DR: RNA/RNA duplex was generally the most stable of the three kinds of duplexes with the same nearest-neighbor sequences and which is more stable between DNA/DNA and RNA/DNA duplexe is sequence dependent.
Journal ArticleDOI
Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.
TL;DR: Structural parameters characterizing the bending propensity of trinucleotides were deduced from DNase I digestion data using simple probabilistic models and are in good agreement with X‐ray crystallographic data on bent DNA.