Proceedings of the National Academy of Sciences, Vol. 99, No. 15. (23 July 2002), pp. 9888-9893. A large fraction of the information content of metazoan genomes resides in the transcriptional and posttranscriptional cis-regulatory elements that collectively provide the blueprint for using the protein-coding capacity of the DNA, thus guiding the development and physiology of the entire organism. As successive whole-genome sequencing projects[---]-including those of mice and humans[---]are completed, we have full access to the regulatory genome of yet another species. But our ability to decipher the cis-regulatory code, and hence to link genes into regulatory networks on a global scale, is currently very limited. Here we describe SCORE (Site Clustering Over Random Expectation), a computational method for identifying transcriptional cis-regulatory modules based on the fact that they often contain, in statistically improbable concentrations, multiple binding sites for th...
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Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.From: citeulike.org
Post Date: 2006-05-16 00:00:00
Nucleic Acids Res, Vol. 31, No. 19. (1 October 2003), pp. 5654-5666. The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing varia...
more An annotation management system for relational databasesFrom: citeulike.org
Post Date: 2006-05-16 00:00:00
We present an annotation management system for relational databases. In this system, every piece of data in a relation is assumed to have zero or more annotations associated with it and annotations are propagated along, from the source to the output, as data is being transformed through a query. Such an annotation management system is important for understanding the provenance and quality of data, especially in applications that deal with integration of scientific and biological data....
more Limit on the Neutrino Mass from the WMAP Three Year DataFrom: citeulike.org
Post Date: 2006-05-16 00:00:00
We derive an upper limit on the neutrino mass from the WMAP three-year data alone by employing a deterministic minimisation method based on a grid search in multi-parameter space. Assuming the flat LCDM model with power-law adiabatic perturbations, we find the sum of m_nu < 2.0 eV in agreement with the result of the WMAP team. This result, the limit being nearly the same as that from the WMAP first-year data, means that the fundamental limit on the neutrino mass obtainable from the cosmi...
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