skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Selection of optimal oligonucleotide probes for microarrays usingmultiple criteria, global alignment and parameter estimation.

Abstract

The oligonucleotide specificity for microarray hybridizationcan be predicted by its sequence identity to non-targets, continuousstretch to non-targets, and/or binding free energy to non-targets. Mostcurrently available programs only use one or two of these criteria, whichmay choose 'false' specific oligonucleotides or miss 'true' optimalprobes in a considerable proportion. We have developed a software tool,called CommOligo using new algorithms and all three criteria forselection of optimal oligonucleotide probes. A series of filters,including sequence identity, free energy, continuous stretch, GC content,self-annealing, distance to the 3'-untranslated region (3'-UTR) andmelting temperature (Tm), are used to check each possibleoligonucleotide. A sequence identity is calculated based on gapped globalalignments. A traversal algorithm is used to generate alignments for freeenergy calculation. The optimal Tm interval is determined based on probecandidates that have passed all other filters. Final probes are pickedusing a combination of user-configurable piece-wise linear functions andan iterative process. The thresholds for identity, stretch and freeenergy filters are automatically determined from experimental data by anaccessory software tool, CommOligo_PE (CommOligo Parameter Estimator).The program was used to design probes for both whole-genome and highlyhomologous sequence data. CommOligo and CommOligo_PE are freely availableto academic users upon request.

Authors:
; ;
Publication Date:
Research Org.:
COLLABORATION - PerkinElmer Life and AnalyticalSciences
OSTI Identifier:
903375
Report Number(s):
LBNL-60475
Journal ID: ISSN 0305-1048; NARHAD; R&D Project: VGTLJK; BnR: KP1102010; TRN: US200720%%307
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Nucleic Acids Research
Additional Journal Information:
Journal Volume: 33; Journal Issue: 19; Related Information: Journal Publication Date: 24 October,2005; Journal ID: ISSN 0305-1048
Country of Publication:
United States
Language:
English
Subject:
59; ALGORITHMS; ALIGNMENT; DESIGN; FREE ENERGY; HYBRIDIZATION; MELTING; OLIGONUCLEOTIDES; PROBES; SPECIFICITY; Microarrays

Citation Formats

Li, Xingyuan, He, Zhili, and Zhou, Jizhong. Selection of optimal oligonucleotide probes for microarrays usingmultiple criteria, global alignment and parameter estimation.. United States: N. p., 2005. Web. doi:10.1093/nar/gki914.
Li, Xingyuan, He, Zhili, & Zhou, Jizhong. Selection of optimal oligonucleotide probes for microarrays usingmultiple criteria, global alignment and parameter estimation.. United States. https://doi.org/10.1093/nar/gki914
Li, Xingyuan, He, Zhili, and Zhou, Jizhong. Sun . "Selection of optimal oligonucleotide probes for microarrays usingmultiple criteria, global alignment and parameter estimation.". United States. https://doi.org/10.1093/nar/gki914.
@article{osti_903375,
title = {Selection of optimal oligonucleotide probes for microarrays usingmultiple criteria, global alignment and parameter estimation.},
author = {Li, Xingyuan and He, Zhili and Zhou, Jizhong},
abstractNote = {The oligonucleotide specificity for microarray hybridizationcan be predicted by its sequence identity to non-targets, continuousstretch to non-targets, and/or binding free energy to non-targets. Mostcurrently available programs only use one or two of these criteria, whichmay choose 'false' specific oligonucleotides or miss 'true' optimalprobes in a considerable proportion. We have developed a software tool,called CommOligo using new algorithms and all three criteria forselection of optimal oligonucleotide probes. A series of filters,including sequence identity, free energy, continuous stretch, GC content,self-annealing, distance to the 3'-untranslated region (3'-UTR) andmelting temperature (Tm), are used to check each possibleoligonucleotide. A sequence identity is calculated based on gapped globalalignments. A traversal algorithm is used to generate alignments for freeenergy calculation. The optimal Tm interval is determined based on probecandidates that have passed all other filters. Final probes are pickedusing a combination of user-configurable piece-wise linear functions andan iterative process. The thresholds for identity, stretch and freeenergy filters are automatically determined from experimental data by anaccessory software tool, CommOligo_PE (CommOligo Parameter Estimator).The program was used to design probes for both whole-genome and highlyhomologous sequence data. CommOligo and CommOligo_PE are freely availableto academic users upon request.},
doi = {10.1093/nar/gki914},
url = {https://www.osti.gov/biblio/903375}, journal = {Nucleic Acids Research},
issn = {0305-1048},
number = 19,
volume = 33,
place = {United States},
year = {2005},
month = {10}
}