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ASTD: The Alternative Splicing and Transcript Diversity database

Item Type:Article
Title:ASTD: The Alternative Splicing and Transcript Diversity database
Creators Name:Koscielny, G. and Texier, V.L. and Gopalakrishnan, C. and Kumanduri, V. and Riethoven, J.J. and Nardone, F. and Stanley, E. and Fallsehr, C. and Hofmann, O. and Kull, M. and Harrington, E. and Boue, S. and Eyras, E. and Plass, M. and Lopez, F. and Ritchie, W. and Moucadel, V. and Ara, T. and Pospisil, H. and Herrmann, A. and Reich, J.G. and Guigo, R. and Bork, P. and Doeberitz, M.V. and Vilo, J. and Hide, W. and Apweiler, R. and Thanaraj, T.A. and Gautheret, D.
Abstract:The Alternative Splicing and Transcript Diversity database (ASTD) gives access to a vast collection of alternative transcripts that integrate transcription initiation, polyadenylation and splicing variant data. Alternative transcripts are derived from the mapping of transcribed sequences to the complete human, mouse and rat genomes using an extension of the computational pipeline developed for the ASD (Alternative Splicing Database) and ATD (Alternative Transcript Diversity) databases, which are now superseded by ASTD. For the human genome, ASTD identifies splicing variants, transcription initiation variants and polyadenylation variants in 68%, 68% and 62% of the gene set, respectively, consistent with current estimates for transcription variation. Users can access ASTD through a variety of browsing and query tools, including expression state-based queries for the identification of tissue-specific isoforms. Participating labs have experimentally validated a subset of ASTD-predicted alternative splice forms and alternative polyadenylation forms that were not previously reported. The ASTD database is accessed at http://www.ebi.ac.uk/astd.
Keywords:Alternative Splicing, Database Management Systems, Genetic Databases, Information Storage and Retrieval, Reproducibility of Results, Software, User-Computer Interface, Animals, Mice, Rats
Publisher:Academic Press
Page Range:213-220
Date:March 2009
Official Publication:https://doi.org/10.1016/j.ygeno.2008.11.003
PubMed:View item in PubMed

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