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Volume 30(1);  January 1, 2002
Articles
The Molecular Biology Database Collection: 2002 update
Andreas D. Baxevanis
Nucleic Acids Res. 2002 January 1; 30(1): 1–12.
PMCID: PMC99169
Database resources of the National Center for Biotechnology Information: 2002 update
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
Nucleic Acids Res. 2002 January 1; 30(1): 13–16.
PMCID: PMC99094
GenBank
Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Barbara A. Rapp, and David L. Wheeler
Nucleic Acids Res. 2002 January 1; 30(1): 17–20.
PMCID: PMC99127
The EMBL Nucleotide Sequence Database
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
Nucleic Acids Res. 2002 January 1; 30(1): 21–26.
PMCID: PMC99098
DNA Data Bank of Japan (DDBJ) for genome scale research in life science
Y. Tateno, T. Imanishi, S. Miyazaki, K. Fukami-Kobayashi, N. Saitou, H. Sugawara, and T. Gojobori
Nucleic Acids Res. 2002 January 1; 30(1): 27–30.
PMCID: PMC99140
MIPS: a database for genomes and protein sequences
H. W. Mewes, D. Frishman, U. Güldener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Münsterkötter, S. Rudd, and B. Weil
Nucleic Acids Res. 2002 January 1; 30(1): 31–34.
PMCID: PMC99165
The Protein Information Resource: an integrated public resource of functional annotation of proteins
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
Nucleic Acids Res. 2002 January 1; 30(1): 35–37.
PMCID: PMC99125
The Ensembl genome database project
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
Nucleic Acids Res. 2002 January 1; 30(1): 38–41.
PMCID: PMC99161
The KEGG databases at GenomeNet
Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, and Akihiro Nakaya
Nucleic Acids Res. 2002 January 1; 30(1): 42–46.
PMCID: PMC99091
BRENDA, enzyme data and metabolic information
Ida Schomburg, Antje Chang, and Dietmar Schomburg
Nucleic Acids Res. 2002 January 1; 30(1): 47–49.
PMCID: PMC99121
EXProt: a database for proteins with an experimentally verified function
Björn M. Ursing, Frank H. J. van Enckevort, Jack A. M. Leunissen, and Roland J. Siezen
Nucleic Acids Res. 2002 January 1; 30(1): 50–51.
PMCID: PMC99155
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
Ada Hamosh, Alan F. Scott, Joanna Amberger, Carol Bocchini, David Valle, and Victor A. McKusick
Nucleic Acids Res. 2002 January 1; 30(1): 52–55.
PMCID: PMC99152
The EcoCyc Database
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
Nucleic Acids Res. 2002 January 1; 30(1): 56–58.
PMCID: PMC99147
The MetaCyc Database
Peter D. Karp, Monica Riley, Suzanne M. Paley, and Alida Pellegrini-Toole
Nucleic Acids Res. 2002 January 1; 30(1): 59–61.
PMCID: PMC99148
SubtiList: the reference database for the Bacillus subtilis genome
Ivan Moszer, Louis M. Jones, Sandrine Moreira, Cécilia Fabry, and Antoine Danchin
Nucleic Acids Res. 2002 January 1; 30(1): 62–65.
PMCID: PMC99059
Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more
Masaki Fumoto, Satoru Miyazaki, and Hideaki Sugawara
Nucleic Acids Res. 2002 January 1; 30(1): 66–68.
PMCID: PMC99149
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
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
Nucleic Acids Res. 2002 January 1; 30(1): 69–72.
PMCID: PMC99086
The TRIPLES database: a community resource for yeast molecular biology
Anuj Kumar, Kei-Hoi Cheung, Nick Tosches, Peter Masiar, Yang Liu, Perry Miller, and Michael Snyder
Nucleic Acids Res. 2002 January 1; 30(1): 73–75.
PMCID: PMC99075
yMGV: helping biologists with yeast microarray data mining
Stéphane Le Crom, Frédéric Devaux, Claude Jacq, and Philippe Marc
Nucleic Acids Res. 2002 January 1; 30(1): 76–79.
PMCID: PMC99164
YPL.db: the Yeast Protein Localization database
Georg Habeler, Klaus Natter, Gerhard G. Thallinger, Matthew E. Crawford, Sepp D. Kohlwein, and Zlatko Trajanoski
Nucleic Acids Res. 2002 January 1; 30(1): 80–83.
PMCID: PMC99114
Genomic database resources for Dictyostelium discoideum
Lisa Kreppel and Alan R. Kimmel
Nucleic Acids Res. 2002 January 1; 30(1): 84–86.
PMCID: PMC99139
PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)
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
Nucleic Acids Res. 2002 January 1; 30(1): 87–90.
PMCID: PMC99106
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome
Heiko Schoof, Paolo Zaccaria, Heidrun Gundlach, Kai Lemcke, Stephen Rudd, Grigory Kolesov, Roland Arnold, H. W. Mewes, and Klaus F. X. Mayer
Nucleic Acids Res. 2002 January 1; 30(1): 91–93.
PMCID: PMC99069
FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants
F. Samson, V. Brunaud, S. Balzergue, B. Dubreucq, L. Lepiniec, G. Pelletier, M. Caboche, and A. Lecharny
Nucleic Acids Res. 2002 January 1; 30(1): 94–97.
PMCID: PMC99145
RiceGAAS: an automated annotation system and database for rice genome sequence
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
Nucleic Acids Res. 2002 January 1; 30(1): 98–102.
PMCID: PMC99141
Gramene: a resource for comparative grass genomics
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
Nucleic Acids Res. 2002 January 1; 30(1): 103–105.
PMCID: PMC99157
The FlyBase database of the Drosophila genome projects and community literature
The FlyBase Consortium
Nucleic Acids Res. 2002 January 1; 30(1): 106–108.
PMCID: PMC99082
Wanda: a database of duplicated fish genes
Yves Van de Peer, John S. Taylor, Jayabalan Joseph, and Axel Meyer
Nucleic Acids Res. 2002 January 1; 30(1): 109–112.
PMCID: PMC99142
The Mouse Genome Database (MGD): the model organism database for the laboratory mouse
Judith A. Blake, Joel E. Richardson, Carol J. Bult, Jim A. Kadin, and Janan T. Eppig
Nucleic Acids Res. 2002 January 1; 30(1): 113–115.
PMCID: PMC99116
FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
Hidemasa Bono, Takeya Kasukawa, Masaaki Furuno, Yoshihide Hayashizaki, and Yasushi Okazaki
Nucleic Acids Res. 2002 January 1; 30(1): 116–118.
PMCID: PMC99137
Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags
Takeshi Kawashima, Shuichi Kawashima, Yuji Kohara, Minoru Kanehisa, and Kazuhiro W. Makabe
Nucleic Acids Res. 2002 January 1; 30(1): 119–120.
PMCID: PMC99134
MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea
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
Nucleic Acids Res. 2002 January 1; 30(1): 121–124.
PMCID: PMC99159
Rat Genome Database (RGD): mapping disease onto the genome
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
Nucleic Acids Res. 2002 January 1; 30(1): 125–128.
PMCID: PMC99132
The Celera Discovery System™
Anthony Kerlavage, Vivien Bonazzi, Matteo di Tommaso, Charles Lawrence, Peter Li, Frank Mayberry, Richard Mural, Marc Nodell, Mark Yandell, Jinghui Zhang, and Paul D. Thomas
Nucleic Acids Res. 2002 January 1; 30(1): 129–136.
PMCID: PMC99167
Annotating the human proteome: the Human Proteome Survey Database (HumanPSD™) and an in-depth target database for G protein-coupled receptors (GPCR-PD™) from Incyte Genomics
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
Nucleic Acids Res. 2002 January 1; 30(1): 137–141.
PMCID: PMC99168
Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes
Claude-Alain H. Roten, Patrick Gamba, Jean-Luc Barblan, and Dimitri Karamata
Nucleic Acids Res. 2002 January 1; 30(1): 142–144.
PMCID: PMC99136
euGenes: a eukaryote genome information system
Donald G. Gilbert
Nucleic Acids Res. 2002 January 1; 30(1): 145–148.
PMCID: PMC99146
Homophila: human disease gene cognates in Drosophila
Samson Chien, Lawrence T. Reiter, Ethan Bier, and Michael Gribskov
Nucleic Acids Res. 2002 January 1; 30(1): 149–151.
PMCID: PMC99119
HOWDY: an integrated database system for human genome research
Mika Hirakawa
Nucleic Acids Res. 2002 January 1; 30(1): 152–157.
PMCID: PMC99130
JSNP: a database of common gene variations in the Japanese population
Mika Hirakawa, Toshihiro Tanaka, Yoichi Hashimoto, Masako Kuroda, Toshihisa Takagi, and Yusuke Nakamura
Nucleic Acids Res. 2002 January 1; 30(1): 158–162.
PMCID: PMC99126
PharmGKB: the Pharmacogenetics Knowledge Base
Micheal Hewett, Diane E. Oliver, Daniel L. Rubin, Katrina L. Easton, Joshua M. Stuart, Russ B. Altman, and Teri E. Klein
Nucleic Acids Res. 2002 January 1; 30(1): 163–165.
PMCID: PMC99138
HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project
Reiko Kikuno, Takahiro Nagase, Mina Waki, and Osamu Ohara
Nucleic Acids Res. 2002 January 1; 30(1): 166–168.
PMCID: PMC99081
Genew: the Human Gene Nomenclature Database
Hester M. Wain, Michael Lush, Fabrice Ducluzeau, and Sue Povey
Nucleic Acids Res. 2002 January 1; 30(1): 169–171.
PMCID: PMC99058
MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002
Marcella Attimonelli, Domenico Catalano, Carmela Gissi, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Monica Santamaria, Graziano Pesole, and Cecilia Saccone
Nucleic Acids Res. 2002 January 1; 30(1): 172–173.
PMCID: PMC99095
Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences
Cecilia Lanave, Flavio Licciulli, Mariateresa De Robertis, Alessandra Marolla, and Marcella Attimonelli
Nucleic Acids Res. 2002 January 1; 30(1): 174–175.
PMCID: PMC99074
5S Ribosomal RNA Database
Maciej Szymanski, Miroslawa Z. Barciszewska, Volker A. Erdmann, and Jan Barciszewski
Nucleic Acids Res. 2002 January 1; 30(1): 176–178.
PMCID: PMC99124
The tmRNA Website: invasion by an intron
Kelly P. Williams
Nucleic Acids Res. 2002 January 1; 30(1): 179–182.
PMCID: PMC99078
The European database on small subunit ribosomal RNA
Jan Wuyts, Yves Van de Peer, Tina Winkelmans, and Rupert De Wachter
Nucleic Acids Res. 2002 January 1; 30(1): 183–185.
PMCID: PMC99113
PALS db: Putative Alternative Splicing database
Y.-H. Huang, Y.-T. Chen, J.-J. Lai, S.-T. Yang, and U.-C. Yang
Nucleic Acids Res. 2002 January 1; 30(1): 186–190.
PMCID: PMC99163
ExInt: an Exon Intron Database
M. Sakharkar, F. Passetti, J. E. de Souza, M. Long, and S. J. de Souza
Nucleic Acids Res. 2002 January 1; 30(1): 191–194.
PMCID: PMC99089
SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data
Julia V. Ponomarenko, Galina V. Orlova, Anatoly S. Frolov, Mikhail S. Gelfand, and Mikhail P. Ponomarenko
Nucleic Acids Res. 2002 January 1; 30(1): 195–199.
PMCID: PMC99084
ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro
Vadim P. Valuev, Dmitry A. Afonnikov, Mikhail P. Ponomarenko, Luciano Milanesi, and Nikolay A. Kolchanov
Nucleic Acids Res. 2002 January 1; 30(1): 200–202.
PMCID: PMC99101
VirOligo: a database of virus-specific oligonucleotides
Kenji Onodera and Ulrich Melcher
Nucleic Acids Res. 2002 January 1; 30(1): 203–204.
PMCID: PMC99087
HERVd: database of human endogenous retroviruses
Jan Pačes, Adam Pavlíček, and Václav Pačes
Nucleic Acids Res. 2002 January 1; 30(1): 205–206.
PMCID: PMC99133
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Ron Edgar, Michael Domrachev, and Alex E. Lash
Nucleic Acids Res. 2002 January 1; 30(1): 207–210.
PMCID: PMC99122
READ: RIKEN Expression Array Database
Hidemasa Bono, Takeya Kasukawa, Yoshihide Hayashizaki, and Yasushi Okazaki
Nucleic Acids Res. 2002 January 1; 30(1): 211–213.
PMCID: PMC99103
HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues
Peter M. Haverty, Zhiping Weng, Nathan L. Best, Kenneth R. Auerbach, Li-Li Hsiao, Roderick V. Jensen, and Steven R. Gullans
Nucleic Acids Res. 2002 January 1; 30(1): 214–217.
PMCID: PMC99144
The human (PEDB) and mouse (mPEDB) Prostate Expression Databases
Peter S. Nelson, Colin Pritchard, Denise Abbott, and Nigel Clegg
Nucleic Acids Res. 2002 January 1; 30(1): 218–220.
PMCID: PMC99083
The Gene Resource Locator: gene locus maps for transcriptome analysis
Toshihiko Honkura, Jun Ogasawara, Tomoyuki Yamada, and Shinichi Morishita
Nucleic Acids Res. 2002 January 1; 30(1): 221–225.
PMCID: PMC99160
FIMM, a database of functional molecular immunology: update 2002
Christian Schönbach, Judice L. Y. Koh, Darren R. Flower, Limsoon Wong, and Vladimir Brusic
Nucleic Acids Res. 2002 January 1; 30(1): 226–229.
PMCID: PMC99079
The DT40 web site: sampling and connecting the genes of a B cell line
Jean-Marie Buerstedde, Hiroshi Arakawa, Akira Watahiki, Piere Piero Carninci, Y. Yoshihide Hayashizaki, Bernhard Korn, and Jiri Plachy
Nucleic Acids Res. 2002 January 1; 30(1): 230–231.
PMCID: PMC99062
IDR: the ImmunoDeficiency Resource
Jouni Väliaho, Marianne Pusa, Tuomo Ylinen, and Mauno Vihinen
Nucleic Acids Res. 2002 January 1; 30(1): 232–234.
PMCID: PMC99120
The PROSITE database, its status in 2002
Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J. A. Sigrist, Kay Hofmann, and Amos Bairoch
Nucleic Acids Res. 2002 January 1; 30(1): 235–238.
PMCID: PMC99105
PRINTS and PRINTS-S shed light on protein ancestry
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
Nucleic Acids Res. 2002 January 1; 30(1): 239–241.
PMCID: PMC99143
Recent improvements to the SMART domain-based sequence annotation resource
Ivica Letunic, Leo Goodstadt, Nicholas J. Dickens, Tobias Doerks, Joerg Schultz, Richard Mott, Francesca Ciccarelli, Richard R. Copley, Chris P. Ponting, and Peer Bork
Nucleic Acids Res. 2002 January 1; 30(1): 242–244.
PMCID: PMC99073
The Protein Data Bank: unifying the archive
John Westbrook, Zukang Feng, Shri Jain, T. N. Bhat, Narmada Thanki, Veerasamy Ravichandran, Gary L. Gilliland, Wolfgang F. Bluhm, Helge Weissig, Douglas S. Greer, Philip E. Bourne, and Helen M. Berman
Nucleic Acids Res. 2002 January 1; 30(1): 245–248.
PMCID: PMC99110
MMDB: Entrez’s 3D-structure database
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
Nucleic Acids Res. 2002 January 1; 30(1): 249–252.
PMCID: PMC99072
The IMB Jena Image Library of Biological Macromolecules: 2002 update
Jan Reichert and Jürgen Sühnel
Nucleic Acids Res. 2002 January 1; 30(1): 253–254.
PMCID: PMC99077
MODBASE, a database of annotated comparative protein structure models
Ursula Pieper, Narayanan Eswar, Ashley C. Stuart, Valentin A. Ilyin, and Andrej Sali
Nucleic Acids Res. 2002 January 1; 30(1): 255–259.
PMCID: PMC99112
ASTRAL compendium enhancements
John-Marc Chandonia, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, and Steven E. Brenner
Nucleic Acids Res. 2002 January 1; 30(1): 260–263.
PMCID: PMC99063
SCOP database in 2002: refinements accommodate structural genomics
Loredana Lo Conte, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, and Alexey G. Murzin
Nucleic Acids Res. 2002 January 1; 30(1): 264–267.
PMCID: PMC99154
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
Julian Gough and Cyrus Chothia
Nucleic Acids Res. 2002 January 1; 30(1): 268–272.
PMCID: PMC99153
The SBASE protein domain library, release 9.0: an online resource for protein domain identification
Kristian Vlahoviček, János Murvai, Endre Barta, and Sándor Pongor
Nucleic Acids Res. 2002 January 1; 30(1): 273–275.
PMCID: PMC99162
The Pfam Protein Families Database
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
Nucleic Acids Res. 2002 January 1; 30(1): 276–280.
PMCID: PMC99071
CDD: a database of conserved domain alignments with links to domain three-dimensional structure
Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, Paul A. Thiessen, Lewis Y. Geer, and Stephen H. Bryant
Nucleic Acids Res. 2002 January 1; 30(1): 281–283.
PMCID: PMC99109
PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies
V. Mallika, Anirban Bhaduri, and R. Sowdhamini
Nucleic Acids Res. 2002 January 1; 30(1): 284–288.
PMCID: PMC99156
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
Shashi B. Pandit, Dilip Gosar, S. Abhiman, S. Sujatha, Sayali S. Dixit, Natasha S. Mhatre, R. Sowdhamini, and N. Srinivasan
Nucleic Acids Res. 2002 January 1; 30(1): 289–293.
PMCID: PMC99061
GTOP: a database of protein structures predicted from genome sequences
Takeshi Kawabata, Satoshi Fukuchi, Keiichi Homma, Motonori Ota, Jiro Araki, Takehiko Ito, Nobuyuki Ichiyoshi, and Ken Nishikawa
Nucleic Acids Res. 2002 January 1; 30(1): 294–298.
PMCID: PMC99104
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein
Antje Krause, Stefan A. Haas, Eivind Coward, and Martin Vingron
Nucleic Acids Res. 2002 January 1; 30(1): 299–300.
PMCID: PMC99107
ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0
M. Michael Gromiha, Hatsuho Uedaira, Jianghong An, Samuel Selvaraj, Ponraj Prabakaran, and Akinori Sarai
Nucleic Acids Res. 2002 January 1; 30(1): 301–302.
PMCID: PMC99068
DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
Ioannis Xenarios, Łukasz Salwínski, Xiaoqun Joyce Duan, Patrick Higney, Sul-Min Kim, and David Eisenberg
Nucleic Acids Res. 2002 January 1; 30(1): 303–305.
PMCID: PMC99070
Predictome: a database of putative functional links between proteins
Joseph C. Mellor, Itai Yanai, Karl H. Clodfelter, Julian Mintseris, and Charles DeLisi
Nucleic Acids Res. 2002 January 1; 30(1): 306–309.
PMCID: PMC99135
Transterm: a database of mRNAs and translational control elements
Grant H. Jacobs, Oliver Rackham, Peter A. Stockwell, Warren Tate, and Chris M. Brown
Nucleic Acids Res. 2002 January 1; 30(1): 310–311.
PMCID: PMC99085
Transcription Regulatory Regions Database (TRRD): its status in 2002
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
Nucleic Acids Res. 2002 January 1; 30(1): 312–317.
PMCID: PMC99088
AraC-XylS database: a family of positive transcriptional regulators in bacteria
Raquel Tobes and Juan L. Ramos
Nucleic Acids Res. 2002 January 1; 30(1): 318–321.
PMCID: PMC99111
The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data
Viviane Praz, Rouaïda Périer, Claude Bonnard, and Philipp Bucher
Nucleic Acids Res. 2002 January 1; 30(1): 322–324.
PMCID: PMC99099
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, and Stephane Rombauts
Nucleic Acids Res. 2002 January 1; 30(1): 325–327.
PMCID: PMC99092
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
Yutaka Suzuki, Riu Yamashita, Kenta Nakai, and Sumio Sugano
Nucleic Acids Res. 2002 January 1; 30(1): 328–331.
PMCID: PMC99097
TRANSCompel®: a database on composite regulatory elements in eukaryotic genes
Olga V. Kel-Margoulis, Alexander E. Kel, Ingmar Reuter, Igor V. Deineko, and Edgar Wingender
Nucleic Acids Res. 2002 January 1; 30(1): 332–334.
PMCID: PMC99108
UTRdb and UTRsite: specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Update 2002
Graziano Pesole, Sabino Liuni, Giorgio Grillo, Flavio Licciulli, Flavio Mignone, Carmela Gissi, and Cecilia Saccone
Nucleic Acids Res. 2002 January 1; 30(1): 335–340.
PMCID: PMC99102
The Histone Database
Steven Sullivan, Daniel W. Sink, Kenneth L. Trout, Izabela Makalowska, Patrick M. Taylor, Andreas D. Baxevanis, and David Landsman
Nucleic Acids Res. 2002 January 1; 30(1): 341–342.
PMCID: PMC99096
MEROPS: the protease database
Neil D. Rawlings, Emmet O’Brien, and Alan J. Barrett
Nucleic Acids Res. 2002 January 1; 30(1): 343–346.
PMCID: PMC99100
PLANT-PIs: a database for plant protease inhibitors and their genes
F. De Leo, M. Volpicella, F. Licciulli, S. Liuni, R. Gallerani, and L. R. Ceci
Nucleic Acids Res. 2002 January 1; 30(1): 347–348.
PMCID: PMC99076
Sentra, a database of signal transduction proteins
Natalia Maltsev, E. Marland, G. X. Yu, S. Bhatnagar, and R. Lusk
Nucleic Acids Res. 2002 January 1; 30(1): 349–350.
PMCID: PMC99115
HOX Pro DB: the functional genomics of hox ensembles
Alexander V. Spirov, Mikhail Borovsky, and Olesya A. Spirova
Nucleic Acids Res. 2002 January 1; 30(1): 351–353.
PMCID: PMC99118
Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences
Chiquito Crasto, Luis Marenco, Perry Miller, and Gordon Shepherd
Nucleic Acids Res. 2002 January 1; 30(1): 354–360.
PMCID: PMC99065
tGRAP, the G-protein coupled receptors mutant database
Øyvind Edvardsen, Anne Lise Reiersen, Margot W. Beukers, and Kurt Kristiansen
Nucleic Acids Res. 2002 January 1; 30(1): 361–363.
PMCID: PMC99129
NUREBASE: database of nuclear hormone receptors
Jorge Duarte, Guy Perrière, Vincent Laudet, and Marc Robinson-Rechavi
Nucleic Acids Res. 2002 January 1; 30(1): 364–368.
PMCID: PMC99117
AngioDB: database of angiogenesis and angiogenesis-related molecules
Tae-Kwon Sohn, Eun-Joung Moon, Seok-Ki Lee, Hwan-Gue Cho, and Kyu-Won Kim
Nucleic Acids Res. 2002 January 1; 30(1): 369–371.
PMCID: PMC99150
S/MARt DB: a database on scaffold/matrix attached regions
Ines Liebich, Jürgen Bode, Matthias Frisch, and Edgar Wingender
Nucleic Acids Res. 2002 January 1; 30(1): 372–374.
PMCID: PMC99064
CSDBase: an interactive database for cold shock domain-containing proteins and the bacterial cold shock response
Michael H. W. Weber, Ingo Fricke, Niclas Doll, and Mohamed A. Marahiel
Nucleic Acids Res. 2002 January 1; 30(1): 375–378.
PMCID: PMC99128
MDB: the Metalloprotein Database and Browser at The Scripps Research Institute
Jesus M. Castagnetto, Sean W. Hennessy, Victoria A. Roberts, Elizabeth D. Getzoff, John A. Tainer, and Michael E. Pique
Nucleic Acids Res. 2002 January 1; 30(1): 379–382.
PMCID: PMC99158
InBase: the Intein Database
Francine B. Perler
Nucleic Acids Res. 2002 January 1; 30(1): 383–384.
PMCID: PMC99080
FUGOID: functional genomics of organellar introns database
Fei Li and David L. Herrin
Nucleic Acids Res. 2002 January 1; 30(1): 385–386.
PMCID: PMC99166
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources
D. Fredman, M. Siegfried, Y. P. Yuan, P. Bork, H. Lehväslaiho, and A. J. Brookes
Nucleic Acids Res. 2002 January 1; 30(1): 387–391.
PMCID: PMC99093
SCOR: a Structural Classification of RNA database
Peter S. Klosterman, Makio Tamura, Stephen R. Holbrook, and Steven E. Brenner
Nucleic Acids Res. 2002 January 1; 30(1): 392–394.
PMCID: PMC99131
NCIR: a database of non-canonical interactions in known RNA structures
Uma Nagaswamy, Maia Larios-Sanz, James Hury, Shakaala Collins, Zhengdong Zhang, Qin Zhao, and George E. Fox
Nucleic Acids Res. 2002 January 1; 30(1): 395–397.
PMCID: PMC99067
GeneNet: a database on structure and functional organisation of gene networks
E. A. Ananko, N. L. Podkolodny, I. L. Stepanenko, E. V. Ignatieva, O. A. Podkolodnaya, and N. A. Kolchanov
Nucleic Acids Res. 2002 January 1; 30(1): 398–401.
PMCID: PMC99151
LIGAND: database of chemical compounds and reactions in biological pathways
Susumu Goto, Yasushi Okuno, Masahiro Hattori, Takaaki Nishioka, and Minoru Kanehisa
Nucleic Acids Res. 2002 January 1; 30(1): 402–404.
PMCID: PMC99090
SWEET-DB: an attempt to create annotated data collections for carbohydrates
Alexander Loß, Peter Bunsmann, Andreas Bohne, Annika Loß, Eberhard Schwarzer, Elke Lang, and Claus-W. von der Lieth
Nucleic Acids Res. 2002 January 1; 30(1): 405–408.
PMCID: PMC99123
CKAAPs DB: a Conserved Key Amino Acid Positions DataBase
Wilfred W. Li, Boojala V. B. Reddy, John G. Tate, Ilya N. Shindyalov, and Philip E. Bourne
Nucleic Acids Res. 2002 January 1; 30(1): 409–411.
PMCID: PMC99066
TTD: Therapeutic Target Database
X. Chen, Z. L. Ji, and Y. Z. Chen
Nucleic Acids Res. 2002 January 1; 30(1): 412–415.
PMCID: PMC99057
RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database
Dag Harmsen, Jörg Rothgänger, Matthias Frosch, and Jürgen Albert
Nucleic Acids Res. 2002 January 1; 30(1): 416–417.
PMCID: PMC99060
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