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eShadow: A tool for comparing closely related sequences (2004) |
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Abstract |
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Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human to primate or mouse to rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualization of the resulting conservation profile. eShadow also includes a versatile optimization module capable of training the underlying Hidden Markov Model to differentially predict functional sequences. This module grants the tool high flexibility in the analysis of multiple sequence alignments and in comparing sequences with different divergence rates. Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements. The eShadow tool is publicly available at http://eshadow.dcode.org/ |
Publication details |
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Cited publications (15) |
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Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels
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Multiple sequence alignment with the Clustal series of programs
- Chenna, Ramu,
- Sugawara, Hideaki,
- Koike, Tadashi,
- Lopez, Rodrigo,
- Gibson, Toby J.,
- Higgins, Desmond G.,
- Thompson, Julie D.
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Strategies and Tools for Whole-Genome Alignments
- Couronne, Olivier,
- Poliakov, Alexander,
- Bray, Nicolas,
- Ishkhanov, Tigran,
- Ryaboy, Dmitriy,
- Rubin, Edward,
- Pachter, Lior,
- Dubchak, Inna
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Regulatory Roles of Conserved Intergenic Domains in Vertebrate Dlx Bigene Clusters
- Ghanem, Noël,
- Jarinova, Olga,
- Amores, Angel,
- Long, Qiaoming,
- Hatch, Gary,
- Park, Byung Keon,
- Rubenstein, John L.R.,
- Ekker, Marc
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Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA
- Hellmann, Ines,
- Zöllner, Sebastian,
- Enard, Wolfgang,
- Ebersberger, Ingo,
- Nickel, Birgit,
- Pääbo, Svante
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The Ensembl genome database project
- Hubbard, T.,
- Barker, D.,
- Birney, E.,
- Cameron, G.,
- Chen, Y.,
- Clark, L.,
- Cox, T.,
- Cuff, J.,
- Curwen, V.,
- Down, T.,
- Durbin, R.,
- Eyras, E.,
- Gilbert, J.,
- Hammond, M.,
- Huminiecki, L.,
- Kasprzyk, A.,
- Lehvaslaiho, H.,
- Lijnzaad, P.,
- Melsopp, C.,
- Mongin, E.,
- Pettett, R.,
- Pocock, M.,
- Potter, S.,
- Rust, A.,
- Schmidt, E.,
- Searle, S.,
- Slater, G.,
- Smith, J.,
- Spooner, W.,
- Stabenau, A.,
- Stalker, J.,
- Stupka, E.,
- Ureta-Vidal, A.,
- Vastrik, I.,
- Clamp, M.
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The UCSC Genome Browser Database
- Karolchik, D.,
- Baertsch, R.,
- Diekhans, M.,
- Furey, T. S.,
- Hinrichs, A.,
- Lu, Y. T.,
- Roskin, K. M.,
- Schwartz, M.,
- Sugnet, C. W.,
- Thomas, D. J.,
- Weber, R. J.,
- Haussler, D.,
- Kent, W. J.
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A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins
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Two methods for improving performance of an HMM and their application for gene finding (1998)
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A comparison of profile hidden Markov model procedures for remote homology detection
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