| 1 | -- | 10 | Andreas D. Baxevanis. The Molecular Biology Database Collection: an updated compilation of biological database resources |
| 11 | -- | 16 | 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, Barbara A. Rapp. Database resources of the National Center for Biotechnology Information |
| 17 | -- | 21 | Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Evelyn Camon, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Vincent Lombard, Rodrigo Lopez, Helen E. Parkinson, Nicole Redaschi, Peter Sterk, Peter Stoehr, Mary Ann Tuli. The EMBL nucleotide sequence database |
| 22 | -- | 28 | Roman L. Tatusov, Darren A. Natale, Igor V. Garkavtsev, Tatiana A. Tatusova, Uma T. Shankavaram, Bachoti S. Rao, Boris Kiryutin, Michael Y. Galperin, Natalie D. Fedorova, Eugene V. Koonin. The COG database: new developments in phylogenetic classification of proteins from complete genomes |
| 29 | -- | 32 | Winona C. Barker, John S. Garavelli, Zhenglin Hou, Hongzhan Huang, Robert S. Ledley, Peter B. McGarvey, Hans-Werner Mewes, Bruce C. Orcutt, Friedhelm Pfeiffer, Akira Tsugita, C. R. Vinayaka, Chunlin Xiao, Lai-Su L. Yeh, Cathy H. Wu. Protein Information Resource: a community resource for expert annotation of protein data |
| 33 | -- | 36 | Evgenia V. Kriventseva, Wolfgang Fleischmann, Evgeni M. Zdobnov, Rolf Apweiler. CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins |
| 37 | -- | 40 | Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Jérôme Gouzy, Henning Hermjakob, Nicolas Hulo, Inge Jonassen, Daniel Kahn, Alexander Kanapin, Youla Karavidopoulou, Rodrigo Lopez, Beate Marx, Nicola J. Mulder, Thomas M. Oinn, Marco Pagni, Florence Servant, Christian J. A. Sigrist, Evgeni M. Zdobnov. The InterPro database, an integrated documentation resource for protein families, domains and functional sites |
| 41 | -- | 43 | Daniel H. Haft, Brendan J. Loftus, Delwood L. Richardson, Fan Yang, Jonathan A. Eisen, Ian T. Paulsen, Owen White. TIGRFAMs: a protein family resource for the functional identification of proteins |
| 44 | -- | 48 | Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Isabelle Phan, Evgeni M. Zdobnov. Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes |
| 49 | -- | 51 | Kevin A. T. Silverstein, Elizabeth Shoop, James E. Johnson, Alan Kilian, John L. Freeman, Timothy M. Kunau, Ihab A. Awad, Margaret Mayer, Ernest F. Retzel. The MetaFam Server: a comprehensive protein family resource |
| 52 | -- | 54 | Cathy H. Wu, Chunlin Xiao, Zhenglin Hou, Hongzhan Huang, Winona C. Barker. iProClass: an integrated, comprehensive and annotated protein classification database |
| 55 | -- | 57 | Sabine Dietmann, Jong Park, Cédric Notredame, Andreas Heger, Michael Lappe, Liisa Holm. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3 |
| 58 | -- | 60 | János Murvai, Kristian Vlahovicek, Endre Barta, Sándor Pongor. The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments |
| 61 | -- | 65 | S. Balaji, S. Sujatha, S. Sai Chetan Kumar, Narayanaswamy Srinivasan. PALI - a database of Phylogeny and ALIgnment of homologous protein structures |
| 70 | -- | 71 | Junichi Watanabe, Masahide Sasaki, Yutaka Suzuki, Sumio Sugano. FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum |
| 72 | -- | 74 | Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Ernesto Pérez-Rueda, César Bonavides-Martínez, Julio Collado-Vides. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12 |
| 75 | -- | 79 | Maria C. Costanzo, Matthew E. Crawford, Jodi E. Hirschman, Janice E. Kranz, Philip Olsen, Laura S. Robertson, Marek S. Skrzypek, Burkhard R. Braun, Kelley Lennon Hopkins, Pinar Kondu, Carey Lengieza, Jodi E. Lew-Smith, Michael Tillberg, James I. Garrels. YPDTM, PombePDTM and WormPDTM: model organism volumes of the BioKnowledgeTM Library, an integrated resource for protein information |
| 80 | -- | 81 | Catherine A. Ball, Heng Jin, Gavin Sherlock, Shuai Weng, John C. Matese, Rey Andrada, Gail Binkley, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Laurie Issel-Tarver, Mark Schroeder, David Botstein, J. Michael Cherry. Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data |
| 82 | -- | 86 | Lincoln Stein, Paul W. Sternberg, Richard Durbin, Jean Thierry-Mieg, John Spieth. WormBase: network access to the genome and biology of Caenorhabditis elegans |
| 87 | -- | 90 | Judy Sprague, Eckehard Doerry, Sarah A. Douglas, Monte Westerfield. The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research |
| 91 | -- | 94 | Judith A. Blake, Janan T. Eppig, Joel E. Richardson, Carol J. Bult, James A. Kadin. The Mouse Genome Database (MGD): integration nexus for the laboratory mouse |
| 95 | -- | 97 | Carol J. Bult, Debra M. Krupke, Dieter Näf, John P. Sundberg, Janan T. Eppig. Web-based access to mouse models of human cancers: the Mouse Tumor Biology (MTB) Database |
| 98 | -- | 101 | Martin Ringwald, Janan T. Eppig, Dale A. Begley, John P. Corradi, Ingeborg J. McCright, Terry F. Hayamizu, David P. Hill, James A. Kadin, Joel E. Richardson. The Mouse Gene Expression Database (GXD) |
| 102 | -- | 105 | Eva Huala, Allan Dickerman, Margarita Garcia-Hernandez, Danforth Weems, Leonore Reiser, Frank LaFond, David Hanley, Donald Kiphart, Mingzhe Zhuang, Wen Huang, Lukas A. Mueller, Debika Bhattacharyya, Devaki Bhaya, Bruno W. S. Sobral, William D. Beavis, David Meinke, Christopher D. Town, Chris Somerville, Seung Yon Rhee. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant |
| 106 | -- | 110 | Jian Hu, Chris Mungall, Andy Law, Richard Papworth, J. Paul Nelson, Alison Brown, Irene Simpson, Shirley Leckie, David W. Burt, Alan L. Hillyard, Alan L. Archibald. The ARKdb: genome databases for farmed and other animals |
| 111 | -- | 113 | Michael Gribskov, Fariba Fana, Jeffrey Harper, Debra A. Hope, Alice C. Harmon, Douglas W. Smith, Frans E. Tax, Guangfa Zhang. PlantsP: a functional genomics database for plant phosphorylation |
| 114 | -- | 117 | Callum J. Bell, Richard A. Dixon, Andrew D. Farmer, H. Raul Flores, Jeff T. Inman, Robert A. Gonzales, Maria J. Harrison, Nancy L. Paiva, Angela D. Scott, Jennifer W. Weller, Gregory D. May. The Medicago Genome Initiative: a model legume database |
| 118 | -- | 119 | Carl A. Price, Ellen M. Reardon. Mendel, a database of nomenclature for sequenced plant genes |
| 120 | -- | 122 | David Lonsdale, Mark L. Crowe, Benjamin Arnold, Benedict C. Arnold. Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names |
| 123 | -- | 125 | Jeremy D. Peterson, Lowell A. Umayam, Tanja Dickinson, Erin K. Hickey, Owen White. The Comprehensive Microbial Resource |
| 126 | -- | 127 | Axel Bernal, Uy Ear, Nikos Kyrpides. Genomes OnLine Database (GOLD): a monitor of genome projects world-wide |
| 128 | -- | 132 | Nelli Shimko, Lin Liu, B. Franz Lang, Gertraud Burger. GOBASE: the organelle genome database |
| 133 | -- | 136 | M. Mar Albà, David Lee, Frances M. G. Pearl, Adrian J. Shepherd, Nigel J. Martin, Christine A. Orengo, Paul Kellam. VIDA: a virus database system for the organization of animal virus genome open reading frames |
| 137 | -- | 140 | Kim D. Pruitt, Donna R. Maglott. RefSeq and LocusLink: NCBI gene-centered resources |
| 141 | -- | 143 | Shaying Zhao. A comprehensive BAC resource |
| 144 | -- | 147 | Michael Morley, Melissa Arcaro, Joshua Burdick, Raluca Yonescu, Thomas Reid, Ilan R. Kirsch, Vivian G. Cheung. GenMapDB: a database of mapped human BAC clones |
| 148 | -- | 151 | Marco Pagni, Christian Iseli, Thomas Junier, Laurent Falquet, C. Victor Jongeneel, Philipp Bucher. trEST, trGEN and Hits: access to databases of predicted protein sequences |
| 152 | -- | 155 | Gavin Sherlock, Tina Hernandez-Boussard, Andrew Kasarskis, Gail Binkley, John C. Matese, Selina S. Dwight, Miroslava Kaloper, Shuai Weng, Heng Jin, Catherine A. Ball, Michael B. Eisen, Paul T. Spellman, Patrick O. Brown, David Botstein, J. Michael Cherry. The Stanford Microarray Database |
| 156 | -- | 158 | Jun Sese, Hitoshi Nikaidou, Shoko Kawamoto, Yuichi Minesaki, Shinichi Morishita, Kousaku Okubo. BodyMap incorporated PCR-based expression profiling data and a gene ranking system |
| 159 | -- | 164 | John Quackenbush, Jennifer Cho, Daniel Lee, Feng Liang, Ingeborg Holt, Svetlana Karamycheva, Babak Parvizi, Geo Pertea, Razvan Sultana, Joseph White. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species |
| 165 | -- | 166 | Patricia Rodriguez-Tomé, Philip Lijnzaad. RHdb: the Radiation Hybrid database |
| 167 | -- | 168 | Fabrizio Damiano, Raffaele Gallerani, Sabino Liuni, Flavio Licciulli, Luigi R. Ceci. PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes |
| 169 | -- | 170 | Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson. SRPDB (Signal Recognition Particle Database) |
| 171 | -- | 172 | Bjarne Knudsen, Jacek Wower, Christian Zwieb, Jan Gorodkin. tmRDB (tmRNA database) |
| 173 | -- | 174 | Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker Jr., Paul Saxman, Ryan J. Farris, George M. Garrity, Gary J. Olsen, Thomas M. Schmidt, James M. Tiedje. The RDP-II (Ribosomal Database Project) |
| 175 | -- | 177 | Jan Wuyts, Peter De Rijk, Yves Van de Peer, Tina Winkelmans, Rupert De Wachter. The European Large Subunit Ribosomal RNA Database |
| 178 | -- | 180 | Jesús García-Martínez, Ignacio Bescós, Jesús Javier Rodríguez-Sala, Francisco Rodríguez-Valera. RISSC: a novel database for ribosomal 16S 23S RNA genes spacer regions |
| 181 | -- | 184 | Joel A. Klappenbach, Paul Saxman, James R. Cole, Thomas M. Schmidt. rrndb: the Ribosomal RNA Operon Copy Number Database |
| 185 | -- | 188 | Henrik T. Yudate, Makiko Suwa, Ryotaro Irie, Hiroshi Matsui, Tetsuo Nishikawa, Yoshitaka Nakamura, Daisuke Yamaguchi, Zhang Zhi Peng, Tomoyuki Yamamoto, Keiichi Nagai, Koji Hayashi, Tetsuji Otsuki, Tomoyasu Sugiyama, Toshio Ota, Yutaka Suzuki, Sumio Sugano, Takao Isogai, Yasuhiko Masuho. HUNT: launch of a full-length cDNA database from the Helix Research Institute |
| 189 | -- | 193 | Volker A. Erdmann, Miroslawa Z. Barciszewska, Maciej Szymanski, Abraham Hochberg, Nathan de Groot, Jan Barciszewski. The non-coding RNAs as riboregulators |
| 194 | -- | 195 | F. H. D. van Batenburg, Alexander P. Gultyaev, C. W. A. Pleij. PseudoBase: structural information on RNA pseudoknots |
| 196 | -- | 198 | Stefan Gräf, Dirk Strothmann, Stefan Kurtz, Gerhard Steger. HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns |
| 199 | -- | 201 | John S. Garavelli, Zhenglin Hou, Nagarajan Pattabiraman, Robert M. Stephens. The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database |
| 202 | -- | 204 | Jimmy Y. Huang, Douglas L. Brutlag. The EMOTIF database |
| 205 | -- | 206 | George Johnson, Tai Te Wu. Kabat Database and its applications: future directions |
| 207 | -- | 209 | Marie-Paule Lefranc. IMGT, the international ImMunoGeneTics database |
| 210 | -- | 213 | James Robinson, Matthew J. Waller, Peter Parham, Julia G. Bodmer, Steven G. E. Marsh. IMGT/HLA Database - a sequence database for the human major histocompatibility complex |
| 214 | -- | 218 | T. N. Bhat, Philip E. Bourne, Zukang Feng, Gary Gilliland, Shri Jain, Veerasamy Ravichandran, Bohdan Schneider, Kata Schneider, Narmada Thanki, Helge Weissig, John D. Westbrook, Helen M. Berman. The PDB data uniformity project |
| 219 | -- | 220 | Tamotsu Noguchi, Hideo Matsuda, Yutaka Akiyama. PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) |
| 221 | -- | 222 | Roman A. Laskowski. PDBsum: summaries and analyses of PDB structures |
| 223 | -- | 227 | Frances M. G. Pearl, Nigel J. Martin, James E. Bray, Daniel W. A. Buchan, Andrew P. Harrison, David Lee, Gabrielle A. Reeves, Adrian J. Shepherd, Ian Sillitoe, Annabel E. Todd, Janet M. Thornton, Christine A. Orengo. A rapid classification protocol for the CATH Domain Database to support structural genomics |
| 228 | -- | 229 | Ilya N. Shindyalov, Philip E. Bourne. A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm |
| 230 | -- | 233 | Wing Lok Abe Kurtz Chiu, Chun Ngai Sze, Lai Nang Ip, Sze Ki Chan, Steve Chik Fun Au-Yeung. NTDB: Thermodynamic Database for Nucleic Acids |
| 234 | -- | 238 | Alan Christoffels, Antoine van Gelder, Gary Greyling, Robert Miller, Tania Hide, Winston A. Hide. STACK: Sequence Tag Alignment and Consensus Knowledgebase |
| 239 | -- | 241 | Ioannis Xenarios, Esteban Fernandez, Lukasz Salwínski, Xiaoqun Joyce Duan, Michael J. Thompson, Edward M. Marcotte, David Eisenberg. DIP: The Database of Interacting Proteins: 2001 update |
| 242 | -- | 245 | Gary D. Bader, Ian Donaldson, Cheryl Wolting, B. F. Francis Ouellette, Tony Pawson, Christopher W. V. Hogue. BIND - The Biomolecular Interaction Network Database |
| 246 | -- | 254 | Tala Bakheet, Mathias Frevel, Bryan R. G. Williams, William Greer, Khalid S. A. Khabar. ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins |
| 255 | -- | 259 | M. Burset, I. A. Seledtsov, Victor V. Solovyev. SpliceDB: database of canonical and non-canonical mammalian splice sites |
| 260 | -- | 263 | Hongkai Ji, Qing Zhou, Fang Wen, Huiyu Xia, Xin Lu, Yanda Li. AsMamDB: an alternative splice database of mammals |
| 264 | -- | 267 | Pavel V. Baranov, Olga L. Gurvich, Olivier Fayet, Marie Françoise Prère, W. Allen Miller, Raymond F. Gesteland, John F. Atkins, Michael C. Giddings. RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression |
| 268 | -- | 269 | Richard J. Roberts, Dana Macelis. REBASE - restriction enzymes and methylases |
| 270 | -- | 274 | Christoph Grunau, Eric Renault, André Rosenthal, Gérard Roizes. MethDB - a public database for DNA methylation data |
| 275 | -- | 276 | Ian M. Morison, Croydon J. Paton, Susan D. Cleverley. The imprinted gene and parent-of-origin effect database |
| 277 | -- | 0 | Ruti Hershberg, Gill Bejerano, Alberto Santos-Zavaleta, Hanah Margalit. PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites |
| 278 | -- | 280 | Takahiro Ishii, Ken-ichi Yoshida, Goro Terai, Yasutaro Fujita, Kenta Nakai. DBTBS: a database of Bacillus subtilis promoters and transcription factors |
| 281 | -- | 283 | Edgar Wingender, Xin Chen, Ellen Fricke, R. Geffers, R. Hehl, Ines Liebich, Mathias Krull, V. Matys, Holger Michael, R. Ohnhäuser, M. Prüß, Frank Schacherer, S. Thiele, S. Urbach. The TRANSFAC system on gene expression regulation |
| 284 | -- | 287 | Julia V. Ponomarenko, Dagmara P. Furman, Anatoly S. Frolov, Nikolay L. Podkolodny, Galina Orlova, Mikhail P. Ponomarenko, Nikolay A. Kolchanov, Akinori Sarai. ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another |
| 288 | -- | 290 | Maciej Szymanski, Marzanna A. Deniziak, Jan Barciszewski. Aminoacyl-tRNA synthetases database |
| 291 | -- | 293 | Sharmila Banerjee-Basu, Daniel W. Sink, Andreas D. Baxevanis. The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information |
| 294 | -- | 295 | Nicolas Le Novère, Jean-Pierre Changeux. LGICdb: the ligand-gated ion channel database |
| 296 | -- | 299 | Rami Kantor, Rhoderick Machekano, Matthew J. Gonzales, Kathryn Dupnik, Jonathan M. Schapiro, Robert W. Shafer. Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs |
| 300 | -- | 302 | Alan E. Levine, David L. Steffen. OrCGDB: a database of genes involved in oral cancer |
| 303 | -- | 304 | Jean-Loup Huret, Philippe Dessen, Alain Bernheim. Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated |
| 305 | -- | 307 | Olivier Cohen, Marie-Ange Mermet, Jacques Demongeot. HC Forum®: a web site based on an international human cytogenetic database |
| 308 | -- | 311 | S. T. Sherry, M.-H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski, K. Sirotkin. dbSNP: the NCBI database of genetic variation |
| 312 | -- | 316 | Julia V. Ponomarenko, Tatyana I. Merkulova, Gennady V. Vasiliev, Zoya B. Levashova, Galina Orlova, Sergey V. Lavryushev, Oleg N. Fokin, Mikhail P. Ponomarenko, Anatoly S. Frolov, Akinori Sarai. rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations |
| 317 | -- | 319 | Michael V. Osier, Kei-Hoi Cheung, Judith R. Kidd, Andrew J. Pakstis, Perry L. Miller, Kenneth K. Kidd. ALFRED: an allele frequency database for diverse populations and DNA polymorphisms - an update |
| 320 | -- | 322 | Christian M. Ruitberg, Dennis J. Reeder, John M. Butler. STRBase: a short tandem repeat DNA database for the human identity testing community |
| 323 | -- | 326 | Anne Bahr, Julie Dawn Thompson, Jean-Claude Thierry, Olivier Poch. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations |
| 327 | -- | 328 | Shinsei Minoshima, Susumu Mitsuyama, Masafumi Ohtsubo, Takashi Kawamura, Sachiko Ito, Sayumi Shibamoto, Fumiaki Ito, Nobuyoshi Shimizu. The KMDB/MutationView: a mutation database for human disease genes |
| 329 | -- | 331 | Wilfred W. Li, Boojala V. B. Reddy, Ilya N. Shindyalov, Philip E. Bourne. CKAAPs DB: a conserved key amino acid positions database |
| 332 | -- | 335 | Catherine A. Cooper, Mathew J. Harrison, Marc R. Wilkins, Nicolle H. Packer. GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources |
| 336 | -- | 339 | Eduardo Gonzalez-Couto, Brian Hayes, Anne Danckaert. The life sciences Global Image Database (GID) |
| 340 | -- | 343 | Lynda B. M. Ellis, C. Douglas Hershberger, Edward M. Bryan, Lawrence P. Wackett. The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes |
| 344 | -- | 345 | Kanako Watanabe, James Nelson, Shigeaki Harayama, Hiroaki Kasai. ICB database: the gyrB database for identification and classification of bacteria |
| 346 | -- | 349 | Florence Horn, Gerrit Vriend, Fred E. Cohen. Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems |