| | Articles The Molecular Biology Database Collection: an online compilation of relevant database resources Andreas D. Baxevanis PMCID: PMC102497 DBcat: a catalog of 500 biological databases Claude Discala, Xavier Benigni, Emmanuel Barillot, and Guy Vaysseix PMCID: PMC102454 Database resources of the National Center for Biotechnology Information David L. Wheeler, Colombe Chappey, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Gregory D. Schuler, Tatiana A. Tatusova, and Barbara A. Rapp PMCID: PMC102437 GenBank Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Barbara A. Rapp, and David L. Wheeler PMCID: PMC102453 The EMBL Nucleotide Sequence Database Wendy Baker, Alexandra van den Broek, Evelyn Camon, Pascal Hingamp, Peter Sterk, Guenter Stoesser, and Mary Ann Tuli PMCID: PMC102461 DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams Yoshio Tateno, Satoru Miyazaki, Motonori Ota, Hideaki Sugawara, and Takashi Gojobori PMCID: PMC102400 KEGG: Kyoto Encyclopedia of Genes and Genomes Minoru Kanehisa and Susumu Goto PMCID: PMC102409 The Genome Sequence DataBase C. Harger, G. Chen, A. Farmer, W. Huang, J. Inman, D. Kiphart, F. Schilkey, M. P. Skupski, and J. Weller PMCID: PMC102463 The COG database: a tool for genome-scale analysis of protein functions and evolution Roman L. Tatusov, Michael Y. Galperin, Darren A. Natale, and Eugene V. Koonin PMCID: PMC102395 MIPS: a database for genomes and protein sequences H. W. Mewes, D. Frishman, C. Gruber, B. Geier, D. Haase, A. Kaps, K. Lemcke, G. Mannhaupt, F. Pfeiffer, C. Schüller, S. Stocker, and B. Weil PMCID: PMC102494 The Protein Information Resource (PIR) Winona C. Barker, John S. Garavelli, Hongzhan Huang, Peter B. McGarvey, Bruce C. Orcutt, Geetha Y. Srinivasarao, Chunlin Xiao, Lai-Su L. Yeh, Robert S. Ledley, Joseph F. Janda, Friedhelm Pfeiffer, Hans-Werner Mewes, Akira Tsugita, and Cathy Wu PMCID: PMC102418 The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 Amos Bairoch and Rolf Apweiler PMCID: PMC102476 ProtoMap: automatic classification of protein sequences and hierarchy of protein families Golan Yona, Nathan Linial, and Michal Linial PMCID: PMC102438 The EcoCyc and MetaCyc databases Peter D. Karp, Monica Riley, Milton Saier, Ian T. Paulsen, Suzanne M. Paley, and Alida Pellegrini-Toole PMCID: PMC102475 EcoGene: a genome sequence database for Escherichia coli K-12 Kenneth E. Rudd PMCID: PMC102481 RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12 Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Frederick R. Blattner, and Julio Collado-Vides PMCID: PMC102478 EMGLib: the Enhanced Microbial Genomes Library (update 2000) Guy Perrière, Philippe Bessières, and Bernard Labedan PMCID: PMC102414 CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000 Yasukazu Nakamura, Takakazu Kaneko, and Satoshi Tabata PMCID: PMC102459 The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information Maria C. Costanzo, Jennifer D. Hogan, Michael E. Cusick, Brian P. Davis, Ann M. Fancher, Peter E. Hodges, Pinar Kondu, Carey Lengieza, Jodi E. Lew-Smith, Carol Lingner, Kevin J. Roberg-Perez, Michael Tillberg, Joan E. Brooks, and James I. Garrels PMCID: PMC102421 Integrating functional genomic information into the Saccharomyces Genome Database Catherine A. Ball, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Laurie Issel-Tarver, Andrew Kasarskis, Charles R. Scafe, Gavin Sherlock, Gail Binkley, Heng Jin, Mira Kaloper, Sidney D. Orr, Mark Schroeder, Shuai Weng, Yan Zhu, David Botstein, and J. Michael Cherry PMCID: PMC102447 TRIPLES: a database of gene function in Saccharomyces cerevisiae Anuj Kumar, Kei-Hoi Cheung, Petra Ross-Macdonald, Paulo S. R. Coelho, Perry Miller, and Michael Snyder PMCID: PMC102388 YIDB: the Yeast Intron DataBase Pascal J. Lopez and Bertrand Séraphin PMCID: PMC102386 The Phytophthora Genome Initiative Database: informatics and analysis for distributed pathogenomic research Mark Waugh, Peter Hraber, Jennifer Weller, Yihe Wu, Guonghong Chen, Jeff Inman, Don Kiphart, and Bruno Sobral PMCID: PMC102488 The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans W. James Kent and Alan M. Zahler PMCID: PMC102389 Gene discovery using the maize genome database ZmDB Xiaowu Gai, Shailesh Lal, Liqun Xing, Volker Brendel, and Virginia Walbot PMCID: PMC102455 INE: a rice genome database with an integrated map view Katsumi Sakata, Baltazar A. Antonio, Yoshiyuki Mukai, Hideki Nagasaki, Yasumichi Sakai, Kazuyoshi Makino, and Takuji Sasaki PMCID: PMC102484 DAtA: Database of Arabidopsis thaliana Annotation Curtis J. Palm, Nancy A. Federspiel, and Ronald W. Davis PMCID: PMC102487 UK CropNet: a collection of databases and bioinformatics resources for crop plant genomics Jo Dicks, Mary Anderson, Linda Cardle, Sam Cartinhour, Matthew Couchman, Guy Davenport, Jeremy Dickson, Mike Gale, David Marshall, Sean May, Hamish McWilliam, Andrew O’Malia, Helen Ougham, Martin Trick, Sean Walsh, and Robbie Waugh PMCID: PMC102397 The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse Judith A. Blake, Janan T. Eppig, Joel E. Richardson, Muriel T. Davisson, and the Mouse Genome Database Group PMCID: PMC102449 Mouse Tumor Biology Database (MTB): enhancements and current status Carol J. Bult, Debra M. Krupke, John P. Sundberg, and Janan T. Eppig PMCID: PMC102417 GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements Martin Ringwald, Janan T. Eppig, James A. Kadin, Joel E. Richardson, and the Gene Expression Database Group PMCID: PMC102464 XREFdb: cross-referencing the genetics and genes of mammals and model organisms R. Ploger, J. Zhang, D. Bassett, R. Reeves, P. Hieter, M. Boguski, and F. Spencer PMCID: PMC102470 WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction Ross Overbeek, Niels Larsen, Gordon D. Pusch, Mark D’Souza, Evgeni Selkov Jr, Nikos Kyrpides, Michael Fonstein, Natalia Maltsev, and Evgeni Selkov PMCID: PMC102471 NCBI’s LocusLink and RefSeq Donna R. Maglott, Kenneth S. Katz, Hugues Sicotte, and Kim D. Pruitt PMCID: PMC102393 Human BAC Ends Shaying Zhao PMCID: PMC102394 MAGEST: MAboya Gene Expression patterns and Sequence Tags Takeshi Kawashima, Shuichi Kawashima, Minoru Kanehisa, Hiroki Nishida, and Kazuhiro W. Makabe PMCID: PMC102485 BodyMap: a human and mouse gene expression database Teruyoshi Hishiki, Shoko Kawamoto, Shinichi Morishita, and Kousaku Okubo PMCID: PMC102396 Axeldb: a Xenopus laevis database focusing on gene expression Nicolas Pollet, Heiko A. Schmidt, Volker Gawantka, Martin Vingron, and Christof Niehrs PMCID: PMC102398 The TIGR Gene Indices: reconstruction and representation of expressed gene sequences John Quackenbush, Feng Liang, Ingeborg Holt, Geo Pertea, and Jonathan Upton PMCID: PMC102391 RHdb: the Radiation Hybrid database Patricia Rodriguez-Tomé and Philip Lijnzaad PMCID: PMC102439 MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status M. Attimonelli, N. Altamura, R. Benne, A. Brennicke, J. M. Cooper, D. D’Elia, A. de Montalvo, B. de Pinto, M. De Robertis, P. Golik, V. Knoop, C. Lanave, J. Lazowska, F. Licciulli, B. S. Malladi, F. Memeo, M. Monnerot, R. Pasimeni, S. Pilbout, A. H. V. Schapira, P. Sloof, and C. Saccone PMCID: PMC102423 Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences Cecilia Lanave, Sabino Liuni, Flavio Licciulli, and Marcella Attimonelli PMCID: PMC102422 MITOP, the mitochondrial proteome database: 2000 update C. Scharfe, P. Zaccaria, K. Hoertnagel, M. Jaksch, T. Klopstock, M. Dembowski, R. Lill, H. Prokisch, K. D. Gerbitz, W. Neupert, H. W. Mewes, and T. Meitinger PMCID: PMC102491 PLMItRNA, a database for tRNAs and tRNA genes in plant mitochondria: enlargement and updating Vito Volpetti, Raffaele Gallerani, Caterina De Benedetto, Sabino Liuni, Flavio Licciulli, and Luigi R. Ceci PMCID: PMC102413 MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins Graziano Pesole, Carmela Gissi, Domenico Catalano, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Marcella Attimonelli, and Cecilia Saccone PMCID: PMC102385 5S ribosomal RNA database Y2K Maciej Szymanski, Miroslawa Z. Barciszewska, Jan Barciszewski, and Volker A. Erdmann PMCID: PMC102473 The tmRNA Website Kelly P. Williams PMCID: PMC102480 tmRDB (tmRNA database) Christian Zwieb and Jacek Wower PMCID: PMC102404 SRPDB (Signal Recognition Particle Database) Christian Zwieb and Tore Samuelsson PMCID: PMC102405 The RDP (Ribosomal Database Project) continues Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker Jr, Paul R. Saxman, Jason M. Stredwick, George M. Garrity, Bing Li, Gary J. Olsen, Sakti Pramanik, Thomas M. Schmidt, and James M. Tiedje PMCID: PMC102428 The European Small Subunit Ribosomal RNA database Yves Van de Peer, Peter De Rijk, Jan Wuyts, Tina Winkelmans, and Rupert De Wachter PMCID: PMC102429 The European Large Subunit Ribosomal RNA database Peter De Rijk, Jan Wuyts, Yves Van de Peer, Tina Winkelmans, and Rupert De Wachter PMCID: PMC102430 The database of the smallest known auto-replicable RNA species: viroids and viroid-like RNAs Martin Pelchat, Patrick Deschênes, and Jean-Pierre Perreault PMCID: PMC102402 The IDB and IEDB: intron sequence and evolution databases Nicholas J. Schisler and Jeffrey D. Palmer PMCID: PMC102469 EID: the Exon–Intron Database—an exhaustive database of protein-coding intron-containing genes Serge Saxonov, Iraj Daizadeh, Alexei Fedorov, and Walter Gilbert PMCID: PMC102483 ExInt: an Exon/Intron database M. Sakharkar, M. Long, T. W. Tan, and S. J. de Souza PMCID: PMC102468 UTRdb and UTRsite: specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs Graziano Pesole, Sabino Liuni, Giorgio Grillo, Flavio Licciulli, Alessandra Larizza, Wojciech Makalowski, and Cecilia Saccone PMCID: PMC102415 Non-coding, mRNA-like RNAs database Y2K Volker A. Erdmann, Maciej Szymanski, Abraham Hochberg, Nathan de Groot, and Jan Barciszewski PMCID: PMC102406 PseudoBase: a database with RNA pseudoknots F. H. D. van Batenburg, A. P. Gultyaev, C. W. A. Pleij, J. Ng, and J. Oliehoek PMCID: PMC102383 SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation Julia V. Ponomarenko, Galina V. Orlova, Mikhail P. Ponomarenko, Sergey V. Lavryushev, Anatoly S. Frolov, Svetlana V. Zybova, and Nikolay A. Kolchanov PMCID: PMC102392 The RESID Database of protein structure modifications: 2000 update John S. Garavelli PMCID: PMC102419 The Prostate Expression Database (PEDB): status and enhancements in 2000 Peter S. Nelson, Nigel Clegg, Burak Eroglu, Victoria Hawkins, Roger Bumgarner, Todd Smith, and Leroy Hood PMCID: PMC102457 Kabat Database and its applications: 30 years after the first variability plot George Johnson and Tai Te Wu PMCID: PMC102431 IMGT, the international ImMunoGeneTics database Manuel Ruiz, Véronique Giudicelli, Chantal Ginestoux, Peter Stoehr, James Robinson, Julia Bodmer, Steven G. E. Marsh, Ronald Bontrop, Marc Lemaitre, Gérard Lefranc, Denys Chaume, and Marie-Paule Lefranc PMCID: PMC102442 FIMM, a database of functional molecular immunology Christian Schönbach, Judice L.Y. Koh, Xin Sheng, Limsoon Wong, and Vladimir Brusic PMCID: PMC102489 PRINTS-S: the database formerly known as PRINTS T. K. Attwood, M. D. R. Croning, D. R. Flower, A. P. Lewis, J. E. Mabey, P. Scordis, J. N. Selley, and W. Wright PMCID: PMC102408 Increased coverage of protein families with the Blocks Database servers Jorja G. Henikoff, Elizabeth A. Greene, Shmuel Pietrokovski, and Steven Henikoff PMCID: PMC102407 SMART: a web-based tool for the study of genetically mobile domains Jörg Schultz, Richard R. Copley, Tobias Doerks, Chris P. Ponting, and Peer Bork PMCID: PMC102444 The Protein Data Bank Helen M. Berman, John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, and Philip E. Bourne PMCID: PMC102472 MMDB: 3D structure data in Entrez Yanli Wang, Kenneth J. Addess, Lewis Geer, Thomas Madej, Aron Marchler-Bauer, Diane Zimmerman, and Stephen H. Bryant PMCID: PMC102448 The IMB Jena Image Library of Biological Macromolecules Jan Reichert, Andreas Jabs, Peter Slickers, and Jürgen Sühnel PMCID: PMC102466 ModBase, a database of annotated comparative protein structure models Roberto Sánchez, Ursula Pieper, Neboja Mirkovi, Paul I. W. de Bakker, Edward Wittenstein, and Andrej ali PMCID: PMC102433 The ASTRAL compendium for protein structure and sequence analysis Steven E. Brenner, Patrice Koehl, and Michael Levitt PMCID: PMC102434 SCOP: a Structural Classification of Proteins database Loredana Lo Conte, Bart Ailey, Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, and Cyrus Chothia PMCID: PMC102479 The SBASE protein domain library, release 7.0: a collection of annotated protein sequence segments János Murvai, Kristian Vlahovicek, Endre Barta, Bruno Cataletto, and Sándor Pongor PMCID: PMC102474 The Pfam Protein Families Database Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, and Erik L. L. Sonnhammer PMCID: PMC102420 ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons Florence Corpet, Florence Servant, Jérôme Gouzy, and Daniel Kahn PMCID: PMC102458 The SYSTERS protein sequence cluster set A. Krause, J. Stoye, and M. Vingron PMCID: PMC102384 ProClass protein family database Hongzhan Huang, Chunlin Xiao, and Cathy H. Wu PMCID: PMC102450 Assigning genomic sequences to CATH Frances M. G. Pearl, David Lee, James E. Bray, Ian Sillitoe, Annabel E. Todd, Andrew P. Harrison, Janet M. Thornton, and Christine A. Orengo PMCID: PMC102424 ProTherm, version 2.0: thermodynamic database for proteins and mutants M. Michael Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira, P. Prabakaran, and Akinori Sarai PMCID: PMC102403 The 1999 SWISS-2DPAGE database update Christine Hoogland, Jean-Charles Sanchez, Luisa Tonella, Pierre-Alain Binz, Amos Bairoch, Denis F. Hochstrasser, and Ron D. Appel PMCID: PMC102456 DIP: the Database of Interacting Proteins Ioannis Xenarios, Danny W. Rice, Lukasz Salwinski, Marisa K. Baron, Edward M. Marcotte, and David Eisenberg PMCID: PMC102387 Codon usage tabulated from international DNA sequence databases: status for the year 2000 Yasukazu Nakamura, Takashi Gojobori, and Toshimichi Ikemura PMCID: PMC102460 Transterm: a database of messenger RNA components and signals Grant H. Jacobs, Peter A. Stockwell, Mark J. Schrieber, Warren P. Tate, and Chris M. Brown PMCID: PMC102492 ASDB: database of alternatively spliced genes I. Dralyuk, M. Brudno, M. S. Gelfand, M. Zorn, and I. Dubchak PMCID: PMC102426 Transcription Regulatory Regions Database (TRRD): its status in 2000 N. A. Kolchanov, O. A. Podkolodnaya, E. A. Ananko, E. V. Ignatieva, I. L. Stepanenko, O. V. Kel-Margoulis, A. E. Kel, T. I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, F. A. Kolpakov, N. L. Podkolodny, A. N. Naumochkin, I. M. Korostishevskaya, A. G. Romashchenko, and G. C. Overton PMCID: PMC102412 The Eukaryotic Promoter Database (EPD) Rouaïda Cavin Périer, Viviane Praz, Thomas Junier, Claude Bonnard, and Philipp Bucher PMCID: PMC102462 The ENZYME database in 2000 Amos Bairoch PMCID: PMC102465 REBASE – restriction enzymes and methylases Richard J. Roberts and Dana Macelis PMCID: PMC102482 Object-oriented Transcription Factors Database (ooTFD) David Ghosh PMCID: PMC102451 COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation Olga V. Kel-Margoulis, Aida G. Romashchenko, Nikolay A. Kolchanov, Edgar Wingender, and Alexander E. Kel PMCID: PMC102399 TRANSFAC: an integrated system for gene expression regulation E. Wingender, X. Chen, R. Hehl, H. Karas, I. Liebich, V. Matys, T. Meinhardt, M. Prüß, I. Reuter, and F. Schacherer PMCID: PMC102445 The Histone Database: a comprehensive WWW resource for histones and histone fold-containing proteins Steven A. Sullivan, L. Aravind, Izabela Makalowska, Andreas D. Baxevanis, and David Landsman PMCID: PMC102427 MEROPS: the peptidase database Neil D. Rawlings and Alan J. Barrett PMCID: PMC102440 Aminoacyl-tRNA synthetases database Y2K Maciej Szymanski and Jan Barciszewski PMCID: PMC102446 The Homeodomain Resource: a prototype database for a large protein family Sharmila Banerjee-Basu, Joseph F. Ryan, and Andreas D. Baxevanis PMCID: PMC102490 HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project Reiko Kikuno, Takahiro Nagase, Mikita Suyama, Mina Waki, Makoto Hirosawa, and Osamu Ohara PMCID: PMC102416 The DExH/D protein family database Eckhard Jankowsky and Anja Jankowsky PMCID: PMC102432 SENTRA, a database of signal transduction proteins Mark D’Souza, Margaret F. Romine, and Natalia Maltsev PMCID: PMC102390 HOX Pro: a specialized database for clusters and networks of homeobox genes Alexander V. Spirov, Timothy Bowler, and John Reinitz PMCID: PMC102436 Olfactory Receptor Database: a sensory chemoreceptor resource Emmanouil Skoufos, Luis Marenco, Prakash M. Nadkarni, Perry L. Miller, and Gordon M. Shepherd PMCID: PMC102443 InBase, the Intein Database Francine B. Perler PMCID: PMC102441 Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database Robert W. Shafer, Duane R. Jung, Bradley J. Betts, Yinong Xi, and Matthew J. Gonzales PMCID: PMC102477 Atlas of Genetics and Cytogenetics in Oncology and Haematology, an Interactive Database Jean-Loup Huret, Sylvaine Le Minor, Franck Dorkeld, Philippe Dessen, and Alain Bernheim PMCID: PMC102493 dbSNP: a database of single nucleotide polymorphisms Elizabeth M. Smigielski, Karl Sirotkin, Minghong Ward, and Stephen T. Sherry PMCID: PMC102496 HGBASE: a database of SNPs and other variations in and around human genes Anthony J. Brookes, Heikki Lehväslaiho, Marianne Siegfried, Jana G. Boehm, Yan P. Yuan, Chandra M. Sarkar, Peer Bork, and Flavio Ortigao PMCID: PMC102467 ALFRED: an allele frequency database for diverse populations and DNA polymorphisms Kei-Hoi Cheung, Michael V. Osier, Judith R. Kidd, Andrew J. Pakstis, Perry L. Miller, and Kenneth K. Kidd PMCID: PMC102486 Keio Mutation Database (KMDB) for human disease gene mutations Shinsei Minoshima, Susumu Mitsuyama, Saho Ohno, Takashi Kawamura, and Nobuyoshi Shimizu PMCID: PMC102495 KinMutBase, a database of human disease-causing protein kinase mutations Kaj A. E. Stenberg, Pentti T. Riikonen, and Mauno Vihinen PMCID: PMC102425 Update of KEYnet: a gene and protein names database for biosequences functional organisation D. Catalano, F. Licciulli, D. D’Elia, and M. Attimonelli PMCID: PMC102452 AAindex: Amino Acid index database Shuichi Kawashima and Minoru Kanehisa PMCID: PMC102411 Database of non-canonical base pairs found in known RNA structures Uma Nagaswamy, Neil Voss, Zhengdong Zhang, and George E. Fox PMCID: PMC102435 The University of Minnesota Biocatalysis/Biodegradation Database: microorganisms, genomics and prediction Lynda B. M. Ellis, C. Douglas Hershberger, and Lawrence P. Wackett PMCID: PMC102401 LIGAND: chemical database of enzyme reactions Susumu Goto, Takaaki Nishioka, and Minoru Kanehisa PMCID: PMC102410 |
