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Your search keyword '"Victor Kunin"' showing total 2 results
Start Over Author "Victor Kunin" Journal bioinformatics (oxford, england)
2 results on '"Victor Kunin"'

1. CoGenT++: an extensive and extensible data environment for computational genomics

Author

Nikos Darzentas, José M. Peregrín-Alvarez, Benjamin Audit, Nuria Lopez-Bigas, Ildefonso Cases, Paul Janssen, Victor Kunin, Anton J. Enright, Mike L. Smith, Sophia Tsoka, Dag Ahrén, Christos A. Ouzounis, Leon Goldovsky, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Laboratory for Microbiology, Centre d'Etude de l'Energie Nucléaire (SCK-CEN), Institute of Agrobiotechnology, National Center for Research and Technology, Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Laboratoire Joliot Curie, École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS), Transcription Networks Group, National Center for Biotechnology, Sanger Institute, Wellcome Trust, École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and École normale supérieure de Lyon (ENS de Lyon)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Statistics and Probability, Ancestral reconstruction, Information Storage and Retrieval, Computational biology, Biology, computational genomics, computer.software_genre, Biochemistry, Genome, 03 medical and health sciences, Consistency (database systems), User-Computer Interface, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Databases, Genetic, Computer Graphics, Molecular Biology, data integration, 030304 developmental biology, 0303 health sciences, 030302 biochemistry & molecular biology, Computational genomics, Chromosome Mapping, Computational Biology, Genome project, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Systems Integration, Computational Mathematics, Gene nomenclature, ComputingMethodologies_PATTERNRECOGNITION, Computational Theory and Mathematics, Database Management Systems, Data mining, computer, Functional genomics, Sequence Analysis, Software, Data integration
Abstract

Motivation: CoGenT++ is a data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility. Description: CoGenT++ facilitates the re-distribution of all fully sequenced and published genomes, storing information about species, gene names and protein sequences. We describe our scalable implementation of ProXSim, a continually updated all-against-all similarity database, which stores pairwise relationships between all genome sequences. Based on these similarities, derived databases are generated for gene fusions---AllFuse, putative orthologs---OFAM, protein families---TRIBES, phylogenetic profiles---ProfUse and phylogenetic trees. Extensions based on the CoGenT++ environment include disease gene prediction, pattern discovery, automated domain detection, genome annotation and ancestral reconstruction. Conclusion: CoGenT++ provides a comprehensive environment for computational genomics, accessible primarily for large-scale analyses as well as manual browsing. Availability: The database and component downloads are accessible at http://cgg.ebi.ac.uk/cogentpp.html. Contact: ouzounis@ebi.ac.uk

Published
2005
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2. MagicMatch--cross-referencing sequence identifiers across databases

Author

Mike L. Smith, Victor Kunin, Leon Goldovsky, Christos A. Ouzounis, and Anton J. Enright

Subjects
Statistics and Probability, Sequence analysis, Computer science, Hash function, Molecular Sequence Data, Information Storage and Retrieval, computer.software_genre, Biochemistry, Software, Sequence Analysis, Protein, Amino Acid Sequence, Insertion sequence, Databases, Protein, Molecular Biology, Sequence (medicine), Database, business.industry, Proteins, Similitude, Computer Science Applications, Identifier, Computational Mathematics, Computational Theory and Mathematics, Checksum, Database Management Systems, Data mining, business, computer, Sequence Alignment, Algorithms
Abstract

Motivation: At present, mapping of sequence identifiers across databases is a daunting, time-consuming and computationally expensive process, usually achieved by sequence similarity searches with strict threshold values. Summary: We present a rapid and efficient method to map sequence identifiers across databases. The method uses the MD5 checksum algorithm for message integrity to generate sequence fingerprints and uses these fingerprints as hash strings to map sequences across databases. The program, called MagicMatch, is able to cross-link any of the major sequence databases within a few seconds on a modest desktop computer. Availability: MagicMatch is available at the following URL (http://cgg.ebi.ac.uk/services/magicmatch/), including an interactive service for major databases and binary downloads for widely used platforms. Contact: ouzounis@ebi.ac.uk

Published
2005

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