Abstract

The Virtual Hybridization approach predicts the most probable hybridization sites across a target nucleic acid of known sequence, including both perfect and mismatched pairings. Potential hybridization sites, having a user-defined minimum number of bases that are paired with the oligonucleotide probe, are first identified. Then free energy values are evaluated for each potential hybridization site, and if it has a calculated free energy of equal or higher negative value than a user-defined free energy cut-off value, it is considered as a site of high probability of hybridization. The Universal Fingerprinting Chip Applications Server contains the software for visualizing predicted hybridization patterns, which yields a simulated hybridization fingerprint that can be compared with experimentally derived fingerprints or with a virtual fingerprint arising from a different sample.Availability http://bioinformatica.homelinux.org/UFCVH/

Highlights

  • Several mathematical models have been widely used to predict thermal stability of oligonucleotide duplexes

  • Whereas empirical methods based on nucleotide composition alone can be used to calculate the thermal stability with reasonable precision, nearest-neighbor (NN) models are better considered for describing thermal stability of oligonucleotide duplexes because this is strongly correlated with sequence variations [1, 2]

  • This server allows web access to the tool called Virtual Hybridization (VH) [8], which is a simulation of the hybridization reaction between the probes and DNA targets, considering thermodynamic data for predicting the stability of the double chain and finding probable sites for hybridization as would happen in real conditions

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Summary

Introduction

Background: Several mathematical models have been widely used to predict thermal stability of oligonucleotide duplexes. Complete sets of NN parameters for energy contributions due to perfect base-pairings, single mismatches, and dangling ends have been published recently [3,4,5]. These thermodynamic parameters provide a basis for predicting the stability of both perfectly paired and mismatch-containing duplex structures.

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