Nucleic Acids Research Advance Access originally published online on November 27, 2006
Nucleic Acids Research 2007 35(Database issue):D61-D65; doi:10.1093/nar/gkl842
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Nucleic Acids Research, 2007, Vol. 35, Database issue D61-D65
Published by Oxford University Press 2006
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
National Center for Biotechnology Information, National Library of Medicine National Institutes of Health Rm 6An.12J, 45 Center Drive, Bethesda, MD 20892-6510, USA
*To whom correspondence should be addressed. Tel: +1 301 435 5898; Fax: +1 301 480 2918; Email: pruitt{at}ncbi.nlm.nih.gov
Received September 20, 2006. Revised October 6, 2006. Accepted October 6, 2006.
NCBI's reference sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. The database includes 3774 organisms spanning prokaryotes, eukaryotes and viruses, and has records for 2 879 860 proteins (RefSeq release 19). RefSeq records integrate information from multiple sources, when additional data are available from those sources and therefore represent a current description of the sequence and its features. Annotations include coding regions, conserved domains, tRNAs, sequence tagged sites (STS), variation, references, gene and protein product names, and database cross-references. Sequence is reviewed and features are added using a combined approach of collaboration and other input from the scientific community, prediction, propagation from GenBank and curation by NCBI staff. The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence.
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M. D. McDowall, M. S. Scott, and G. J. Barton PIPs: human protein-protein interaction prediction database Nucleic Acids Res., January 1, 2009; 37(suppl_1): D651 - D656. [Abstract] [Full Text] [PDF]
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R. M. Kuhn, D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, M. Pheasant, et al. The UCSC Genome Browser Database: update 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D755 - D761. [Abstract] [Full Text] [PDF]
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M. Shionyu, A. Yamaguchi, K. Shinoda, K.-i. Takahashi, and M. Go AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse Nucleic Acids Res., January 1, 2009; 37(suppl_1): D305 - D309. [Abstract] [Full Text] [PDF]
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T. J. P. Hubbard, B. L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, et al. Ensembl 2009 Nucleic Acids Res., January 1, 2009; 37(suppl_1): D690 - D697. [Abstract] [Full Text] [PDF]
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N. Axelrod, Y. Lin, P. C. Ng, T. B. Stockwell, J. Crabtree, J. Huang, E. Kirkness, R. L. Strausberg, M. E. Frazier, J. C. Venter, et al. The HuRef Browser: a web resource for individual human genomics Nucleic Acids Res., January 1, 2009; 37(suppl_1): D1018 - D1024. [Abstract] [Full Text] [PDF]
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E. M. Muro, R. Herrington, S. Janmohamed, C. Frelin, M. A. Andrade-Navarro, and N. N. Iscove Identification of gene 3' ends by automated EST cluster analysis PNAS, December 23, 2008; 105(51): 20286 - 20290. [Abstract] [Full Text] [PDF]
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S. J. Diskin, M. Li, C. Hou, S. Yang, J. Glessner, H. Hakonarson, M. Bucan, J. M. Maris, and K. Wang Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms Nucleic Acids Res., November 1, 2008; 36(19): e126 - e126. [Abstract] [Full Text] [PDF]
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