Information theoretical probe selection for hybridisation experiments
نویسندگان
چکیده
MOTIVATION The choice of probes is an important feature of hybridisation experiments. In this paper we present an algorithm that optimises probes with respect to a training set of sequences based on Shannon entropy as a quality criterion. The practical motivation for our algorithm is oligonucleotide fingerprinting, a method for the simultaneous identification of sequences (cDNA or genomic DNA) by their hybridisation tags according to a set of short probes such as octamers, although the algorithm is of course not restricted to that application. RESULTS We can show that our method is superior to the selection of probes according to their frequencies, which is a widely used strategy, and to randomly chosen probe sets. The quality of probe sets is assessed by a simulation pipeline that entails the set of probes as a simulation parameter. The performance of probe sets trained on sequences from different organisms shows additionally that probes should be chosen with regard to the organism under analysis. Case studies are presented on how constraints (G+C-content, complexity of the individual probes) influence the selection process. AVAILABILITY A description of the oligonucleotide fingerprinting pipeline is published on our web-page http://www.molgen.mpg.de/ approximately ag_onf/met.htm. An executable of the algorithm and probe lists designed for human and rodents can be downloaded from the ftp-site ftp://ftp.molgen.mpg.de/pub/mpimg/probe_design/.
منابع مشابه
Probe-Fed Rectangular Dielectric Resonator Antennas,Theoretical Modeling and Experiments
A Rectangular Dielectric Resonator Antenna (RDRA) is theoretically analyzed using the Conventional Dielectric Waveguide Model (CDWM), numerically simulated using the High Frequency Structure Simulator (HFSS) based on the Finite Element Method (FEM) software package and experimentally investigated with the consideration of the fundamental mode TE 111. Antenna parameters under investigation inclu...
متن کاملImproved procedures for immobilisation of oligonucleotides on gold-coated piezoelectric quartz crystals.
The high sensitivity and specificity of DNA hybridisation techniques makes them powerful tools for environmental or clinical analysis. This work describes the development of a DNA piezoelectric biosensor for the detection of the hybridisation reaction. Attention was focused on the choice of the coating chemistry that could be used for the immobilisation of oligonucleotides onto the gold surface...
متن کاملA Novel Cassette Method for Probe Evaluation in the Designed Biochips
A critical step in biochip design is the selection of probes with identical hybridisation characteristics. In this article we describe a novel method for evaluating DNA hybridisation probes, allowing the fine-tuning of biochips, that uses cassettes with multiple probes. Each cassette contains probes in equimolar proportions so that their hybridisation performance can be assessed in a single rea...
متن کاملApplications of multiplex ligation-dependent probe amplification (MLPA) method in diagnosis of cancer and genetic disorders
Introduction: Lots of human diseases and syndromes result from partial or complete gene deletions and duplications or changes of certain specific chromosomal sequences. Many various methods are used to study the chromosomal aberrations including Comparative Genomic Hybridization (CGH), Fluorescent in Situ Hybridization (FISH), Southern blots, Multiplex Amplifiable Probe Hybridisation (MAP...
متن کاملSpecificity assessment from fractionation experiments (SAFE): a novel method to evaluate microarray probe specificity based on hybridisation stringencies.
The cDNA-chip technology is a highly versatile tool for the comprehensive analysis of gene expression at the transcript level. Although it has been applied successfully in expression profiling projects, there is an ongoing dispute concerning the quality of such expression data. The latter critically depends on the specificity of hybridisation. SAFE (specificity assessment from fractionation exp...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bioinformatics
دوره 16 10 شماره
صفحات -
تاریخ انتشار 2000