Probe design for large-scale molecular biology applications

V. VanBuren, T. Yoshikawa, Toshio Hamatani, Minoru Ko

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Large-scale molecular biology technologies such as DNA microarrays and large-scale in situ hybridization (ISH) are used to gain an appreciation of global attributes in biological tissues and cells. Although many of these efforts use cDNA probes, an approach that makes use of designed oligo probes should offer improved consistency at uniform hybridization conditions and improved specificity, as demonstrated by various oligo microarray platforms. We describe a new Web-based application that takes FASTA-formatted sequences as input, and returns both a list of the best choices for probes and a full report containing possible alternatives. Probe design for microarrays may use a scoring routine that optimizes probe intensity based upon an artificial neural network (ANN) trained to predict the average probe intensity from the physical properties of the probe and a screen for possible cross-reactivity. This new tool should provide a reliable way to construct probes that maximize signal intensity while minimizing cross-reactivity.

Original languageEnglish
Title of host publicationProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages502-503
Number of pages2
ISBN (Print)0769520006, 9780769520001
DOIs
Publication statusPublished - 2003
Externally publishedYes
Event2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States
Duration: 2003 Aug 112003 Aug 14

Other

Other2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
CountryUnited States
CityStanford
Period03/8/1103/8/14

Fingerprint

Molecular biology
Microarrays
DNA
Physical properties
Tissue
Neural networks

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Science Applications

Cite this

VanBuren, V., Yoshikawa, T., Hamatani, T., & Ko, M. (2003). Probe design for large-scale molecular biology applications. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 (pp. 502-503). [1227388] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSB.2003.1227388

Probe design for large-scale molecular biology applications. / VanBuren, V.; Yoshikawa, T.; Hamatani, Toshio; Ko, Minoru.

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 502-503 1227388.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

VanBuren, V, Yoshikawa, T, Hamatani, T & Ko, M 2003, Probe design for large-scale molecular biology applications. in Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003., 1227388, Institute of Electrical and Electronics Engineers Inc., pp. 502-503, 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, Stanford, United States, 03/8/11. https://doi.org/10.1109/CSB.2003.1227388
VanBuren V, Yoshikawa T, Hamatani T, Ko M. Probe design for large-scale molecular biology applications. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc. 2003. p. 502-503. 1227388 https://doi.org/10.1109/CSB.2003.1227388
VanBuren, V. ; Yoshikawa, T. ; Hamatani, Toshio ; Ko, Minoru. / Probe design for large-scale molecular biology applications. Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. pp. 502-503
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