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

An empirical comparison of tools for phylogenetic footprinting

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

3 Author(s)
Blanchette, M. ; Dept. of Comput. Sci. & Eng., Univ. of Washington, Seattle, WA, USA ; Kwong, S. ; Tompa, M.

Phylogenetic footprinting is an increasingly popular comparative genomics method for detecting regulatory elements in DNA sequences. With the profusion of possible methods to use for phylogenetic footprinting, the biologist needs some guidance to choose the most appropriate tool. We present methods for comparing tools on phylogenetic footprinting data. More specifically, we discuss two different classes of comparative experiments: those on simulated data and those on real orthologous promoter regions. We then report the results of a series of such empirical comparisons. The tools compared are the alignment-based methods using ClustalW and Dialign, and the motif-finding programs MEME and FootPrinter. Our results show that methods taking the species' phylogenetic relationships into consideration obtain better accuracy.

Published in:

Bioinformatics and Bioengineering, 2003. Proceedings. Third IEEE Symposium on

Date of Conference:

10-12 March 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.