Cart (Loading....) | Create Account
Close category search window
 

Fast and sensitive probe selection for DNA chips using jumps in matching statistics

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$31 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

1 Author(s)
Rahmann, S. ; Dept. of Computational Molecular Biol, Max-Planck-Inst. fur Molecular Genetics, Berlin, Germany

The design of large scale DNA microarrays is a challenging problem. So far, probe selection algorithms must trade the ability to cope with large scale problems for a loss of accuracy in the estimation of probe quality. We present an approach based on jumps in matching statistics that combines the best of both worlds. This article consists of two parts. The first part is theoretical. We introduce the notion of jumps in matching statistics between two strings and derive their properties. We estimate the frequency of jumps for random strings in a nonuniform Bernoulli model and present a new heuristic argument to find the center of the length distribution of the longest substring that two random strings have in common. The results are generalized to near-perfect matches with a small number of mismatches. In the second part, we use the concept of jumps to improve the accuracy of the longest common factor approach for probe selection by moving from a string-based to an energy-based specificity measure, while only slightly more than doubling the selection time.

Published in:

Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE

Date of Conference:

11-14 Aug. 2003

Need Help?


IEEE Advancing Technology for Humanity About IEEE Xplore | Contact | Help | Terms of Use | Nondiscrimination Policy | Site Map | Privacy & Opting Out of Cookies

A not-for-profit organization, IEEE is the world's largest professional association for the advancement of technology.
© Copyright 2014 IEEE - All rights reserved. Use of this web site signifies your agreement to the terms and conditions.