Probe design for large-scale molecular biology applications

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

研究成果: Conference contribution


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.

ホスト出版物のタイトルProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
出版社Institute of Electrical and Electronics Engineers Inc.
ISBN(印刷版)0769520006, 9780769520001
出版ステータスPublished - 2003
イベント2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States
継続期間: 2003 8 112003 8 14


Other2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
CountryUnited States

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Science Applications

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