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

doi:https://doi.org/10.1093/nar/gki914

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

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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:: Li, Xingyuan; He, Zhili; Zhou, Jizhong

Publication Date:: 2005-10-30

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.

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                    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

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                    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.

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@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}

}

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