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EID: Exon-Intron Database


NAR Molecular Biology Database Collection entry number 32
Fedorov A.1, Shepelev V.2
1Department of Medicine and Program in Bioinformatics and Proteomics/Genomics, Medical University of Ohio, Toledo, OH 43614, USA.
2Department of Bioinformatics, Institute of Molecular Genetics, RAS, Moscow 123182, Russia.

Database Description

The Exon-Intron Database (EID), publicly available since 2000, is a flat-file, Fasta-formated collection of sequences and annotations for all exons and introns obtained from GenBank. The primary goal of EID is to offer a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. New innovations in EID have been implemented in 2005. The collection of exons and introns has been extended beyond coding regions and current versions of EID contain data on untranslated regions of gene sequences as well. Intron-less genes are included as a special part of EID. For species with entirely sequenced genomes, species-specific databases have been generated. Currently, these species-specific sets of all introns and all exons are available for human, mouse, rat, dog, chicken, zebrafish, fruit fly, worm (C. elegans), and mouse-ear cress (A. thaliana). This list will be extended on a monthly basis in accordance with GenBank updates. EID is freely available at http://www.meduohio.edu/bioinfo/eid/.

Acknowledgements

Support for this work was provided by the Medical University of Ohio Foundation and the Stranahan Foundation, through the Program in Bioinformatics and Proteomics/Genomics. We would like to thank Robert Blumenthal and Peter Bazeley, Medical University of Ohio, for discussion and suggestions on our database.

References

1. Saxonov, S., Daizadeh, I., Fedorov, A. and Gilbert, W. (2000) EID: The Exon-Intron Database: An exhaustive database of protein-containing genes. Nucl. Acids Res., 28, 185-190.
2. Fedorov, A., Stombaugh, J., Harr, M.W., Yu, S., Nasalean, L. and Shepelev, V. (2005) Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database. Nucl. Acids Res., 33, 4578-4583.


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