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FootPrinter2.1
Web Server:
A program for phylogenetic footprinting Download FootPrinter2.1 Sample output Phylogenetic footprinting is a method that identifies putative regulatory elements in DNA sequences. It identifies regions of DNA that are unusually well conserved across a set of orthologous sequences. If you use this software for your publications, please read and cite:
MicroFootPrinter is a front end to the FootPrinter phylogenetic footprinting program, but with specific focus on prokaryotic genomes. You supply a prokaryotic species and gene of interest. MicroFootPrinter will then find related prokaryotes each containing a homologous gene, and run FootPrinter to identify motifs in the regulatory region of your chosen gene that are well conserved across these homologous genes. If you use this software for your publications, please read and cite: Neph, S. and Tompa, M., MicroFootPrinter: a Tool for Phylogenetic Footprinting in Prokaryotic Genomes. Nucleic Acids Research, vol. 34, July 2006, W366-W368.
YMF
and FindExplanators Web Server:
An enumerative motif discovery program.
YMF identifies motifs (made of IUPAC symbols) that occur unsually often in a given set of sequences. FindExplanators extracts from that set of motifs a smaller set of independent motifs. If you use this software for your publications, please read and cite:
StatSigMA computes the statistical significance of multiple sequence alignments (of either nucleotide or amino acid sequences), much as BLAST's E-values provide statistical significance for pairwise alignments. If you use this software for your publications, please read and cite: Prakash, A. and Tompa, M., Statistics of local multiple alignments. 13th Annual International Conference on Intelligent Systems for Molecular Biology, Detroit, MI, June 2005. Bioinformatics, vol. 21, June 2005, i344 - i350. PhyME: Motif discovery in data sets that include both intraspecies overrepresentation and interspecies conservation PhyME discovers motifs by integrating two important aspects of the motif's significance, overrepresentation and interspecies conservation, into one probabilistic score. The algorithm is based on multiple alignment and expectation-maximization. If you use this software for your publications, please read and cite: Sinha, S., Blanchette, M., and Tompa, M. PhyME: A Probabilistic Algorithm for Finding Motifs in Sets of Orthologous Sequences. BMC Bioinformatics, vol. 5, 2004, 170. COSMO: Binding sites in coding regions COSMO is a program that detects putative binding sites in coding regions.Given a set of orthologous mRNA sequences, it identifies regions whose conservation cannot be explained solely by the selective pressure on the protein encoded. If you use this software for your publications, please read and cite: Blanchette, M. A comparative analysis method for detecting binding sites in coding regions. In Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB03), Berlin, 2003. Projection: A motif discovery program based on random projections If you use this software for your publications, please read and cite:
Dapple: Image analysis software for DNA microarrays Dapple is a program for quantitating spots on a two-color DNA microarray image. Given a pair of images from a comparative hybridization, Dapple finds the individual spots on the image, evaluates their qualities, and quantifies their total fluorescent intensities. If you use this software for your publications, please read and cite:
Buhler, J., Ideker, T., and Haynor, D.
Dapple: Improved Techniques
for Finding Spots on DNA Microarrays.
UW CSE Technical Report 2000-08-05.
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