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Articles on comparative genomics in yeasts:
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Paul Cliften, Priya Sudarsanam, Ashwin Desikan, Lucinda Fulton, Bob
Fulton, John Majors, Robert Waterston, Barak A. Cohen, and Mark Johnston,
Finding
Functional Features in Saccharomyces Genomes by Phylogenetic
Footprinting.
Science, Vol. 301, Issue 5629, 71-76, 4 July 2003.
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Manolis Kellis, Nick Patterson, Matthew Endrizzi, Bruce Birren, and Eric
S. Lander,
Sequencing
and comparison of yeast species to identify genes and regulatory elements.
Nature, Vol. 423, 241 - 254, 15 May 2003.
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Chiang DY, Moses AM, Kellis M, Lander ES, and Eisen MB,
Phylogenetically and spatially conserved word pairs associated with
gene-expression changes in yeasts.
Genome Biology, Vol. 4, R43, 26 June 2003.
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Chen-Shan Chin, Jeffrey H. Chuang, and Hao Li,
Genome-wide regulatory complexity in yeast promoters: Separation
of functionally conserved and neutral sequence.
Genome Research, Vol. 15, 205-213, February 2005.
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ClustalW:
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Thompson, J.D., Higgins, D.G., and Gibson, T.J., "CLUSTAL W:
improving the sensitivity of progressive multiple sequence alignment
through sequence weighting, position-specific gap penalties and weight
matrix choice". Nucleic Acids Research 22:4673-4680, 1994.
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MLAGAN
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Michael Brudno, Chuong B. Do, Gregory M. Cooper, Michael F. Kim,
Eugene Davydov, NISC Comparative Sequencing Program, Eric D. Green,
Arend Sidow, and Serafim Batzoglou,
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple
Alignment of Genomic DNA.
Genome Research, Vol. 13, Issue 4, 721-731, April 2003.
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TBA
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Mathieu Blanchette, W. James Kent, Cathy Riemer, Laura Elnitski, Arian
F.A. Smit, Krishna M. Roskin, Robert Baertsch, Kate Rosenbloom, Hiram
Clawson, Eric D. Green, David Haussler, and Webb Miller,
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner.
Genome Research 14:708-715, 2004.
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FootPrinter
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Blanchette, M. and Tompa, M.
FootPrinter: a program designed for phylogenetic footprinting.
Nucleic Acids Research,
vol. 31, no. 13, 2003, 3840-3842.
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Blanchette, M. and Tompa, M.
Discovery of Regulatory Elements by a Computational Method for
Phylogenetic Footprinting.
Genome Research,
vol. 12, no. 5, May 2002, 739-748.
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Blanchette, M., Schwikowski, B., and Tompa, M.
Algorithms for Phylogenetic Footprinting.
Journal of Computational Biology, vol. 9, no. 2, 2002, 211-223.
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Presentation
describing the problem and algorithms underlying FootPrinter.
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