NDLI: An empirical comparison of tools for phylogenetic footprinting

Content Provider	IEEE Xplore Digital Library
Author	Blanchette, M. Kwong, S. Tompa, M.
Copyright Year	2003
Description	Author affiliation: Dept. of Comput. Sci. & Eng., Univ. of Washington, Seattle, WA, USA (Blanchette, M.; Kwong, S.; Tompa, M.)
Abstract	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.
Sponsorship	IEEE Comput. Soc. Inf. Technol. Res. Inst. at Wright State Univ. IEEE Neural Networks Soc
Starting Page	69
Ending Page	78
File Size	750199
Page Count	10
File Format	PDF
ISBN	0769519075
DOI	10.1109/BIBE.2003.1188931
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2003-03-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Phylogeny
Content Type	Text
Resource Type	Article

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