Nucleic Acids Research

Editorial:

Editorial
Nucl. Acids Res. 2002 30: 0; doi:10.1093/nar/30.1.0 [Print PDF] [Request Permissions]  

Articles:

Andreas D. Baxevanis

The Molecular Biology Database Collection: 2002 update
Nucl. Acids Res. 2002 30: 1-12; doi:10.1093/nar/30.1.1 [Abstract] [FREE Full Text] [Print PDF] [Database Listing] [Request Permissions]  

David L. Wheeler, Deanna M. Church, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Tatiana A. Tatusova, Lukas Wagner, and Barbara A. Rapp

Database resources of the National Center for Biotechnology Information: 2002 update
Nucl. Acids Res. 2002 30: 13-16; doi:10.1093/nar/30.1.13 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Barbara A. Rapp, and David L. Wheeler

GenBank
Nucl. Acids Res. 2002 30: 17-20; doi:10.1093/nar/30.1.17 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Evelyn Camon, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Nicole Redaschi, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, and Robert Vaughan

The EMBL Nucleotide Sequence Database
Nucl. Acids Res. 2002 30: 21-26; doi:10.1093/nar/30.1.21 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Y. Tateno, T. Imanishi, S. Miyazaki, K. Fukami-Kobayashi, N. Saitou, H. Sugawara, and T. Gojobori

DNA Data Bank of Japan (DDBJ) for genome scale research in life science
Nucl. Acids Res. 2002 30: 27-30; doi:10.1093/nar/30.1.27 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

H. W. Mewes, D. Frishman, U. Güldener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Münsterkötter, S. Rudd, and B. Weil

MIPS: a database for genomes and protein sequences
Nucl. Acids Res. 2002 30: 31-34; doi:10.1093/nar/30.1.31 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Cathy H. Wu, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhang-Zhi Hu, Robert S. Ledley, Kali C. Lewis, Hans-Werner Mewes, Bruce C. Orcutt, Baris E. Suzek, Akira Tsugita, C. R. Vinayaka, Lai-Su L. Yeh, Jian Zhang, and Winona C. Barker

The Protein Information Resource: an integrated public resource of functional annotation of proteins
Nucl. Acids Res. 2002 30: 35-37; doi:10.1093/nar/30.1.35 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

T. Hubbard, D. Barker, E. Birney, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, L. Huminiecki, A. Kasprzyk, H. Lehvaslaiho, P. Lijnzaad, C. Melsopp, E. Mongin, R. Pettett, M. Pocock, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik, and M. Clamp

The Ensembl genome database project
Nucl. Acids Res. 2002 30: 38-41; doi:10.1093/nar/30.1.38 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, and Akihiro Nakaya

The KEGG databases at GenomeNet
Nucl. Acids Res. 2002 30: 42-46; doi:10.1093/nar/30.1.42 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ida Schomburg, Antje Chang, and Dietmar Schomburg

BRENDA, enzyme data and metabolic information
Nucl. Acids Res. 2002 30: 47-49; doi:10.1093/nar/30.1.47 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Björn M. Ursing, Frank H. J. van Enckevort, Jack A. M. Leunissen, and Roland J. Siezen

EXProt: a database for proteins with an experimentally verified function
Nucl. Acids Res. 2002 30: 50-51; doi:10.1093/nar/30.1.50 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ada Hamosh, Alan F. Scott, Joanna Amberger, Carol Bocchini, David Valle, and Victor A. McKusick

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
Nucl. Acids Res. 2002 30: 52-55; doi:10.1093/nar/30.1.52 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter D. Karp, Monica Riley, Milton Saier, Ian T. Paulsen, Julio Collado-Vides, Suzanne M. Paley, Alida Pellegrini-Toole, César Bonavides, and Socorro Gama-Castro

The EcoCyc Database
Nucl. Acids Res. 2002 30: 56-58; doi:10.1093/nar/30.1.56 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter D. Karp, Monica Riley, Suzanne M. Paley, and Alida Pellegrini-Toole

The MetaCyc Database
Nucl. Acids Res. 2002 30: 59-61; doi:10.1093/nar/30.1.59 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ivan Moszer, Louis M. Jones, Sandrine Moreira, Cécilia Fabry, and Antoine Danchin

SubtiList: the reference database for the Bacillus subtilis genome
Nucl. Acids Res. 2002 30: 62-65; doi:10.1093/nar/30.1.62 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Masaki Fumoto, Satoru Miyazaki, and Hideaki Sugawara

Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more
Nucl. Acids Res. 2002 30: 66-68; doi:10.1093/nar/30.1.66 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Selina S. Dwight, Midori A. Harris, Kara Dolinski, Catherine A. Ball, Gail Binkley, Karen R. Christie, Dianna G. Fisk, Laurie Issel-Tarver, Mark Schroeder, Gavin Sherlock, Anand Sethuraman, Shuai Weng, David Botstein, and J. Michael Cherry

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
Nucl. Acids Res. 2002 30: 69-72; doi:10.1093/nar/30.1.69 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anuj Kumar, Kei-Hoi Cheung, Nick Tosches, Peter Masiar, Yang Liu, Perry Miller, and Michael Snyder

The TRIPLES database: a community resource for yeast molecular biology
Nucl. Acids Res. 2002 30: 73-75; doi:10.1093/nar/30.1.73 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Stéphane Le Crom, Frédéric Devaux, Claude Jacq, and Philippe Marc

yMGV: helping biologists with yeast microarray data mining
Nucl. Acids Res. 2002 30: 76-79; doi:10.1093/nar/30.1.76 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Georg Habeler, Klaus Natter, Gerhard G. Thallinger, Matthew E. Crawford, Sepp D. Kohlwein, and Zlatko Trajanoski

YPL.db: the Yeast Protein Localization database
Nucl. Acids Res. 2002 30: 80-83; doi:10.1093/nar/30.1.80 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Lisa Kreppel and Alan R. Kimmel

Genomic database resources for Dictyostelium discoideum
Nucl. Acids Res. 2002 30: 84-86; doi:10.1093/nar/30.1.84 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Amit Bahl, Brian Brunk, Ross L. Coppel, Jonathan Crabtree, Sharon J. Diskin, Martin J. Fraunholz, Gregory R. Grant, Dinesh Gupta, Robert L. Huestis, Jessica C. Kissinger, Philip Labo, Li Li, Shannon K. McWeeney, Arthur J. Milgram, David S. Roos, Jonathan Schug, and Christian J. Stoeckert, Jr

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)
Nucl. Acids Res. 2002 30: 87-90; doi:10.1093/nar/30.1.87 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Heiko Schoof, Paolo Zaccaria, Heidrun Gundlach, Kai Lemcke, Stephen Rudd, Grigory Kolesov, Roland Arnold, H. W. Mewes, and Klaus F. X. Mayer

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome
Nucl. Acids Res. 2002 30: 91-93; doi:10.1093/nar/30.1.91 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

F. Samson, V. Brunaud, S. Balzergue, B. Dubreucq, L. Lepiniec, G. Pelletier, M. Caboche, and A. Lecharny

FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants
Nucl. Acids Res. 2002 30: 94-97; doi:10.1093/nar/30.1.94 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Katsumi Sakata, Yoshiaki Nagamura, Hisataka Numa, Baltazar A. Antonio, Hideki Nagasaki, Atsuko Idonuma, Wakako Watanabe, Yuji Shimizu, Ikuo Horiuchi, Takashi Matsumoto, Takuji Sasaki, and Kenichi Higo

RiceGAAS: an automated annotation system and database for rice genome sequence
Nucl. Acids Res. 2002 30: 98-102; doi:10.1093/nar/30.1.98 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Doreen Ware, Pankaj Jaiswal, Junjian Ni, Xiaokang Pan, Kuan Chang, Kenneth Clark, Leonid Teytelman, Steve Schmidt, Wei Zhao, Samuel Cartinhour, Susan McCouch, and Lincoln Stein

Gramene: a resource for comparative grass genomics
Nucl. Acids Res. 2002 30: 103-105; doi:10.1093/nar/30.1.103 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

The FlyBase Consortium

The FlyBase database of the Drosophila genome projects and community literature
Nucl. Acids Res. 2002 30: 106-108; doi:10.1093/nar/30.1.106 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yves Van de Peer, John S. Taylor, Jayabalan Joseph, and Axel Meyer

Wanda: a database of duplicated fish genes
Nucl. Acids Res. 2002 30: 109-112; doi:10.1093/nar/30.1.109 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Judith A. Blake, Joel E. Richardson, Carol J. Bult, Jim A. Kadin, Janan T. Eppig, and The Mouse Genome Database Group

The Mouse Genome Database (MGD): the model organism database for the laboratory mouse
Nucl. Acids Res. 2002 30: 113-115; doi:10.1093/nar/30.1.113 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hidemasa Bono, Takeya Kasukawa, Masaaki Furuno, Yoshihide Hayashizaki, and Yasushi Okazaki

FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
Nucl. Acids Res. 2002 30: 116-118; doi:10.1093/nar/30.1.116 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Takeshi Kawashima, Shuichi Kawashima, Yuji Kohara, Minoru Kanehisa, and Kazuhiro W. Makabe

Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags
Nucl. Acids Res. 2002 30: 119-120; doi:10.1093/nar/30.1.119 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stanton L. Martin, Barbara P. Blackmon, Ravi Rajagopalan, Thomas D. Houfek, Robert G. Sceeles, Sheila O. Denn, Thomas K. Mitchell, Douglas E. Brown, Rod A. Wing, and Ralph A. Dean

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea
Nucl. Acids Res. 2002 30: 121-124; doi:10.1093/nar/30.1.121 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Simon Twigger, Jian Lu, Mary Shimoyama, Dan Chen, Dean Pasko, Hanping Long, Jessica Ginster, Chin-Fu Chen, Rajni Nigam, Anne Kwitek, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Howard Jacob, and Peter J. Tonellato

Rat Genome Database (RGD): mapping disease onto the genome
Nucl. Acids Res. 2002 30: 125-128; doi:10.1093/nar/30.1.125 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Anthony Kerlavage, Vivien Bonazzi, Matteo di Tommaso, Charles Lawrence, Peter Li, Frank Mayberry, Richard Mural, Marc Nodell, Mark Yandell, Jinghui Zhang, and Paul Thomas

The Celera Discovery System^TM
Nucl. Acids Res. 2002 30: 129-136; doi:10.1093/nar/30.1.129 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter E. Hodges, Pauline M. Carrico, Jennifer D. Hogan, Kathy E. O’Neill, J. J. Owen, Mary Mangan, Brian P. Davis, Joan E. Brooks, and James I. Garrels

Annotating the human proteome: the Human Proteome Survey Database (HumanPSD^TM) and an in-depth target database for G protein-coupled receptors (GPCR-PD^TM) from Incyte Genomics
Nucl. Acids Res. 2002 30: 137-141; doi:10.1093/nar/30.1.137 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Claude-Alain H. Roten, Patrick Gamba, Jean-Luc Barblan, and Dimitri Karamata

Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes
Nucl. Acids Res. 2002 30: 142-144; doi:10.1093/nar/30.1.142 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Donald G. Gilbert

euGenes: a eukaryote genome information system
Nucl. Acids Res. 2002 30: 145-148; doi:10.1093/nar/30.1.145 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Samson Chien, Lawrence T. Reiter, Ethan Bier, and Michael Gribskov

Homophila: human disease gene cognates in Drosophila
Nucl. Acids Res. 2002 30: 149-151; doi:10.1093/nar/30.1.149 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mika Hirakawa

HOWDY: an integrated database system for human genome research
Nucl. Acids Res. 2002 30: 152-157; doi:10.1093/nar/30.1.152 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Mika Hirakawa, Toshihiro Tanaka, Yoichi Hashimoto, Masako Kuroda, Toshihisa Takagi, and Yusuke Nakamura

JSNP: a database of common gene variations in the Japanese population
Nucl. Acids Res. 2002 30: 158-162; doi:10.1093/nar/30.1.158 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Micheal Hewett, Diane E. Oliver, Daniel L. Rubin, Katrina L. Easton, Joshua M. Stuart, Russ B. Altman, and Teri E. Klein

PharmGKB: the Pharmacogenetics Knowledge Base
Nucl. Acids Res. 2002 30: 163-165; doi:10.1093/nar/30.1.163 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Reiko Kikuno, Takahiro Nagase, Mina Waki, and Osamu Ohara

HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project
Nucl. Acids Res. 2002 30: 166-168; doi:10.1093/nar/30.1.166 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hester M. Wain, Michael Lush, Fabrice Ducluzeau, and Sue Povey

Genew: the Human Gene Nomenclature Database
Nucl. Acids Res. 2002 30: 169-171; doi:10.1093/nar/30.1.169 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Marcella Attimonelli, Domenico Catalano, Carmela Gissi, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Monica Santamaria, Graziano Pesole, and Cecilia Saccone

MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002
Nucl. Acids Res. 2002 30: 172-173; doi:10.1093/nar/30.1.172 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Cecilia Lanave, Flavio Licciulli, Mariateresa De Robertis, Alessandra Marolla, and Marcella Attimonelli

Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences
Nucl. Acids Res. 2002 30: 174-175; doi:10.1093/nar/30.1.174 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maciej Szymanski, Miroslawa Z. Barciszewska, Volker A. Erdmann, and Jan Barciszewski

5S Ribosomal RNA Database
Nucl. Acids Res. 2002 30: 176-178; doi:10.1093/nar/30.1.176 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kelly P. Williams

The tmRNA Website: invasion by an intron
Nucl. Acids Res. 2002 30: 179-182; doi:10.1093/nar/30.1.179 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jan Wuyts, Yves Van de Peer, Tina Winkelmans, and Rupert De Wachter

The European database on small subunit ribosomal RNA
Nucl. Acids Res. 2002 30: 183-185; doi:10.1093/nar/30.1.183 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Y.-H. Huang, Y.-T. Chen, J.-J. Lai, S.-T. Yang, and U.-C. Yang

PALS db: Putative Alternative Splicing database
Nucl. Acids Res. 2002 30: 186-190; doi:10.1093/nar/30.1.186 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

M. Sakharkar, F. Passetti, J. E. de Souza, M. Long, and S. J. de Souza

ExInt: an Exon Intron Database
Nucl. Acids Res. 2002 30: 191-194; doi:10.1093/nar/30.1.191 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Julia V. Ponomarenko, Galina V. Orlova, Anatoly S. Frolov, Mikhail S. Gelfand, and Mikhail P. Ponomarenko

SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data
Nucl. Acids Res. 2002 30: 195-199; doi:10.1093/nar/30.1.195 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Vadim P. Valuev, Dmitry A. Afonnikov, Mikhail P. Ponomarenko, Luciano Milanesi, and Nikolay A. Kolchanov

ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro
Nucl. Acids Res. 2002 30: 200-202; doi:10.1093/nar/30.1.200 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Kenji Onodera and Ulrich Melcher

VirOligo: a database of virus-specific oligonucleotides
Nucl. Acids Res. 2002 30: 203-204; doi:10.1093/nar/30.1.203 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jan Paces, Adam Pavlícek, and Václav Paces

HERVd: database of human endogenous retroviruses
Nucl. Acids Res. 2002 30: 205-206; doi:10.1093/nar/30.1.205 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ron Edgar, Michael Domrachev, and Alex E. Lash

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Nucl. Acids Res. 2002 30: 207-210; doi:10.1093/nar/30.1.207 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hidemasa Bono, Takeya Kasukawa, Yoshihide Hayashizaki, and Yasushi Okazaki

READ: RIKEN Expression Array Database
Nucl. Acids Res. 2002 30: 211-213; doi:10.1093/nar/30.1.211 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter M. Haverty, Zhiping Weng, Nathan L. Best, Kenneth R. Auerbach, Li-Li Hsiao, Roderick V. Jensen, and Steven R. Gullans

HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues
Nucl. Acids Res. 2002 30: 214-217; doi:10.1093/nar/30.1.214 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter S. Nelson, Colin Pritchard, Denise Abbott, and Nigel Clegg

The human (PEDB) and mouse (mPEDB) Prostate Expression Databases
Nucl. Acids Res. 2002 30: 218-220; doi:10.1093/nar/30.1.218 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Toshihiko Honkura, Jun Ogasawara, Tomoyuki Yamada, and Shinichi Morishita

The Gene Resource Locator: gene locus maps for transcriptome analysis
Nucl. Acids Res. 2002 30: 221-225; doi:10.1093/nar/30.1.221 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christian Schönbach, Judice L. Y. Koh, Darren R. Flower, Limsoon Wong, and Vladimir Brusic

FIMM, a database of functional molecular immunology: update 2002
Nucl. Acids Res. 2002 30: 226-229; doi:10.1093/nar/30.1.226 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jean-Marie Buerstedde, Hiroshi Arakawa, Akira Watahiki, Piere Piero Carninci, Y. Yoshihide Hayashizaki, Bernhard Korn, and Jiri Plachy

The DT40 web site: sampling and connecting the genes of a B cell line
Nucl. Acids Res. 2002 30: 230-231; doi:10.1093/nar/30.1.230 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jouni Väliaho, Marianne Pusa, Tuomo Ylinen, and Mauno Vihinen

IDR: the ImmunoDeficiency Resource
Nucl. Acids Res. 2002 30: 232-234; doi:10.1093/nar/30.1.232 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J. A. Sigrist, Kay Hofmann, and Amos Bairoch

The PROSITE database, its status in 2002
Nucl. Acids Res. 2002 30: 235-238; doi:10.1093/nar/30.1.235 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

T. K. Attwood, M. J. Blythe, D. R. Flower, A. Gaulton, J. E. Mabey, N. Maudling, L. McGregor, A. L. Mitchell, G. Moulton, K. Paine, and P. Scordis

PRINTS and PRINTS-S shed light on protein ancestry
Nucl. Acids Res. 2002 30: 239-241; doi:10.1093/nar/30.1.239 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ivica Letunic, Leo Goodstadt, Nicholas J. Dickens, Tobias Doerks, Joerg Schultz, Richard Mott, Francesca Ciccarelli, Richard R. Copley, Chris P. Ponting, and Peer Bork

Recent improvements to the SMART domain-based sequence annotation resource
Nucl. Acids Res. 2002 30: 242-244; doi:10.1093/nar/30.1.242 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

John Westbrook, Zukang Feng, Shri Jain, T. N. Bhat, Narmada Thanki, Veerasamy Ravichandran, Gary L. Gilliland, Wolfgang Bluhm, Helge Weissig, Douglas S. Greer, Philip E. Bourne, and Helen M. Berman

The Protein Data Bank: unifying the archive
Nucl. Acids Res. 2002 30: 245-248; doi:10.1093/nar/30.1.245 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yanli Wang, John B. Anderson, Jie Chen, Lewis Y. Geer, Siqian He, David I. Hurwitz, Cynthia A. Liebert, Thomas Madej, Gabriele H. Marchler, Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, and Stephen H. Bryant

MMDB: Entrez’s 3D-structure database
Nucl. Acids Res. 2002 30: 249-252; doi:10.1093/nar/30.1.249 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jan Reichert and Jürgen Sühnel

The IMB Jena Image Library of Biological Macromolecules: 2002 update
Nucl. Acids Res. 2002 30: 253-254; doi:10.1093/nar/30.1.253 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ursula Pieper, Narayanan Eswar, Ashley C. Stuart, Valentin A. Ilyin, and Andrej Sali

MODBASE, a database of annotated comparative protein structure models
Nucl. Acids Res. 2002 30: 255-259; doi:10.1093/nar/30.1.255 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

John-Marc Chandonia, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, and Steven E. Brenner

ASTRAL compendium enhancements
Nucl. Acids Res. 2002 30: 260-263; doi:10.1093/nar/30.1.260 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Loredana Lo Conte, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, and Alexey G. Murzin

SCOP database in 2002: refinements accommodate structural genomics
Nucl. Acids Res. 2002 30: 264-267; doi:10.1093/nar/30.1.264 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Julian Gough and Cyrus Chothia

SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
Nucl. Acids Res. 2002 30: 268-272; doi:10.1093/nar/30.1.268 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kristian Vlahovicek, János Murvai, Endre Barta, and Sándor Pongor

The SBASE protein domain library, release 9.0: an online resource for protein domain identification
Nucl. Acids Res. 2002 30: 273-275; doi:10.1093/nar/30.1.273 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alex Bateman, Ewan Birney, Lorenzo Cerruti, Richard Durbin, Laurence Etwiller, Sean R. Eddy, Sam Griffiths-Jones, Kevin L. Howe, Mhairi Marshall, and Erik L. L. Sonnhammer

The Pfam Protein Families Database
Nucl. Acids Res. 2002 30: 276-280; doi:10.1093/nar/30.1.276 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, Paul A. Thiessen, Lewis Y. Geer, and Stephen H. Bryant

CDD: a database of conserved domain alignments with links to domain three-dimensional structure
Nucl. Acids Res. 2002 30: 281-283; doi:10.1093/nar/30.1.281 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

V. Mallika, Anirban Bhaduri, and R. Sowdhamini

PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies
Nucl. Acids Res. 2002 30: 284-288; doi:10.1093/nar/30.1.284 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shashi B. Pandit, Dilip Gosar, S. Abhiman, S. Sujatha, Sayali S. Dixit, Natasha S. Mhatre, R. Sowdhamini, and N. Srinivasan

SUPFAM—a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes
Nucl. Acids Res. 2002 30: 289-293; doi:10.1093/nar/30.1.289 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Takeshi Kawabata, Satoshi Fukuchi, Keiichi Homma, Motonori Ota, Jiro Araki, Takehiko Ito, Nobuyuki Ichiyoshi, and Ken Nishikawa

GTOP: a database of protein structures predicted from genome sequences
Nucl. Acids Res. 2002 30: 294-298; doi:10.1093/nar/30.1.294 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Antje Krause, Stefan A. Haas, Eivind Coward, and Martin Vingron

SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein
Nucl. Acids Res. 2002 30: 299-300; doi:10.1093/nar/30.1.299 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

M. Michael Gromiha, Hatsuho Uedaira, Jianghong An, Samuel Selvaraj, Ponraj Prabakaran, and Akinori Sarai

ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0
Nucl. Acids Res. 2002 30: 301-302; doi:10.1093/nar/30.1.301 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ioannis Xenarios, Lukasz Salwínski, Xiaoqun Joyce Duan, Patrick Higney, Sul-Min Kim, and David Eisenberg

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
Nucl. Acids Res. 2002 30: 303-305; doi:10.1093/nar/30.1.303 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Joseph C. Mellor, Itai Yanai, Karl H. Clodfelter, Julian Mintseris, and Charles DeLisi

Predictome: a database of putative functional links between proteins
Nucl. Acids Res. 2002 30: 306-309; doi:10.1093/nar/30.1.306 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Grant H. Jacobs, Oliver Rackham, Peter A. Stockwell, Warren Tate, and Chris M. Brown

Transterm: a database of mRNAs and translational control elements
Nucl. Acids Res. 2002 30: 310-311; doi:10.1093/nar/30.1.310 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

N. A. Kolchanov, E. V. Ignatieva, E. A. Ananko, O. A. Podkolodnaya, I. L. Stepanenko, T. I. Merkulova, M. A. Pozdnyakov, N. L. Podkolodny, A. N. Naumochkin, and A. G. Romashchenko

Transcription Regulatory Regions Database (TRRD): its status in 2002
Nucl. Acids Res. 2002 30: 312-317; doi:10.1093/nar/30.1.312 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Raquel Tobes and Juan L. Ramos

AraC-XylS database: a family of positive transcriptional regulators in bacteria
Nucl. Acids Res. 2002 30: 318-321; doi:10.1093/nar/30.1.318 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Viviane Praz, Rouaïda Périer, Claude Bonnard, and Philipp Bucher

The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data
Nucl. Acids Res. 2002 30: 322-324; doi:10.1093/nar/30.1.322 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, and Stephane Rombauts

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
Nucl. Acids Res. 2002 30: 325-327; doi:10.1093/nar/30.1.325 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yutaka Suzuki, Riu Yamashita, Kenta Nakai, and Sumio Sugano

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
Nucl. Acids Res. 2002 30: 328-331; doi:10.1093/nar/30.1.328 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Olga V. Kel-Margoulis, Alexander E. Kel, Ingmar Reuter, Igor V. Deineko, and Edgar Wingender

TRANSCompel^®: a database on composite regulatory elements in eukaryotic genes
Nucl. Acids Res. 2002 30: 332-334; doi:10.1093/nar/30.1.332 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Graziano Pesole, Sabino Liuni, Giorgio Grillo, Flavio Licciulli, Flavio Mignone, Carmela Gissi, and Cecilia Saccone

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002
Nucl. Acids Res. 2002 30: 335-340; doi:10.1093/nar/30.1.335 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Steven Sullivan, Daniel W. Sink, Kenneth L. Trout, Izabela Makalowska, Patrick M. Taylor, Andreas D. Baxevanis, and David Landsman

The Histone Database
Nucl. Acids Res. 2002 30: 341-342; doi:10.1093/nar/30.1.341 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Neil D. Rawlings, Emmet O’Brien, and Alan J. Barrett

MEROPS: the protease database
Nucl. Acids Res. 2002 30: 343-346; doi:10.1093/nar/30.1.343 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

F. De Leo, M. Volpicella, F. Licciulli, S. Liuni, R. Gallerani, and L. R. Ceci

PLANT-PIs: a database for plant protease inhibitors and their genes
Nucl. Acids Res. 2002 30: 347-348; doi:10.1093/nar/30.1.347 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Natalia Maltsev, E. Marland, G. X. Yu, S. Bhatnagar, and R. Lusk

Sentra, a database of signal transduction proteins
Nucl. Acids Res. 2002 30: 349-350; doi:10.1093/nar/30.1.349 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Alexander V. Spirov, Mikhail Borovsky, and Olesya A. Spirova

HOX Pro DB: the functional genomics of hox ensembles
Nucl. Acids Res. 2002 30: 351-353; doi:10.1093/nar/30.1.351 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Chiquito Crasto, Luis Marenco, Perry Miller, and Gordon Shepherd

Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences
Nucl. Acids Res. 2002 30: 354-360; doi:10.1093/nar/30.1.354 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Øyvind Edvardsen, Anne Lise Reiersen, Margot W. Beukers, and Kurt Kristiansen

tGRAP, the G-protein coupled receptors mutant database
Nucl. Acids Res. 2002 30: 361-363; doi:10.1093/nar/30.1.361 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jorge Duarte, Guy Perrière, Vincent Laudet, and Marc Robinson-Rechavi

NUREBASE: database of nuclear hormone receptors
Nucl. Acids Res. 2002 30: 364-368; doi:10.1093/nar/30.1.364 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tae-Kwon Sohn, Eun-Joung Moon, Seok-Ki Lee, Hwan-Gue Cho, and Kyu-Won Kim

AngioDB: database of angiogenesis and angiogenesis-related molecules
Nucl. Acids Res. 2002 30: 369-371; doi:10.1093/nar/30.1.369 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ines Liebich, Jürgen Bode, Matthias Frisch, and Edgar Wingender

S/MARt DB: a database on scaffold/matrix attached regions
Nucl. Acids Res. 2002 30: 372-374; doi:10.1093/nar/30.1.372 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael H. W. Weber, Ingo Fricke, Niclas Doll, and Mohamed A. Marahiel

CSDBase: an interactive database for cold shock domain-containing proteins and the bacterial cold shock response
Nucl. Acids Res. 2002 30: 375-378; doi:10.1093/nar/30.1.375 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jesus M. Castagnetto, Sean W. Hennessy, Victoria A. Roberts, Elizabeth D. Getzoff, John A. Tainer, and Michael E. Pique

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute
Nucl. Acids Res. 2002 30: 379-382; doi:10.1093/nar/30.1.379 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Francine B. Perler

InBase: the Intein Database
Nucl. Acids Res. 2002 30: 383-384; doi:10.1093/nar/30.1.383 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Fei Li and David L. Herrin

FUGOID: functional genomics of organellar introns database