TY - GEN
T1 - Probe design for large-scale molecular biology applications
AU - VanBuren, V.
AU - Yoshikawa, T.
AU - Hamatani, T.
AU - Ko, M. S.H.
N1 - Publisher Copyright:
© 2003 IEEE.
PY - 2003
Y1 - 2003
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84960460270&partnerID=8YFLogxK
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U2 - 10.1109/CSB.2003.1227388
DO - 10.1109/CSB.2003.1227388
M3 - Conference contribution
AN - SCOPUS:84960460270
T3 - Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
SP - 502
EP - 503
BT - Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
Y2 - 11 August 2003 through 14 August 2003
ER -