| | Articles Nucleic Acids Res. 2003 January 1; 31(1): 0. PMCID: PMC167138 The Molecular Biology Database Collection: 2003 update Andreas D. Baxevanis Nucleic Acids Res. 2003 January 1; 31(1): 1–12. PMCID: PMC165567 DNA Data Bank of Japan (DDBJ) in XML S. Miyazaki, H. Sugawara, T. Gojobori, and Y. Tateno Nucleic Acids Res. 2003 January 1; 31(1): 13–16. PMCID: PMC165535 The EMBL Nucleotide Sequence Database: major new developments Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Francesco Nardone, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, and Robert Vaughan Nucleic Acids Res. 2003 January 1; 31(1): 17–22. PMCID: PMC165468 GenBank Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler Nucleic Acids Res. 2003 January 1; 31(1): 23–27. PMCID: PMC165504 Database resources of the National Center for Biotechnology David L. Wheeler, Deanna M. Church, Scott Federhen, Alex E. Lash, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tatiana A. Tatusova, and Lukas Wagner Nucleic Acids Res. 2003 January 1; 31(1): 28–33. PMCID: PMC165480 NCBI Reference Sequence Project: update and current status Kim D. Pruitt, Tatiana Tatusova, and Donna R. Maglott Nucleic Acids Res. 2003 January 1; 31(1): 34–37. PMCID: PMC165558 Ensembl 2002: accommodating comparative genomics M. Clamp, D. Andrews, D. Barker, P. Bevan, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, T. Hubbard, A. Kasprzyk, D. Keefe, H. Lehvaslaiho, V. Iyer, C. Melsopp, E. Mongin, R. Pettett, 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 E. Birney Nucleic Acids Res. 2003 January 1; 31(1): 38–42. PMCID: PMC165530 The European Bioinformatics Institute's data resources Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola Mulder, Claire O'Donovan, Helen Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, and Graham Cameron Nucleic Acids Res. 2003 January 1; 31(1): 43–50. PMCID: PMC165513 The UCSC Genome Browser Database D. Karolchik, R. Baertsch, M. Diekhans, T. S. Furey, A. Hinrichs, Y. T. Lu, K. M. Roskin, M. Schwartz, C. W. Sugnet, D. J. Thomas, R. J. Weber, D. Haussler, and W. J. Kent Nucleic Acids Res. 2003 January 1; 31(1): 51–54. PMCID: PMC165576 CORG: a database for COmparative Regulatory Genomics C. Dieterich, H. Wang, K. Rateitschak, H. Luz, and M. Vingron Nucleic Acids Res. 2003 January 1; 31(1): 55–57. PMCID: PMC165454 MBGD: microbial genome database for comparative analysis Ikuo Uchiyama Nucleic Acids Res. 2003 January 1; 31(1): 58–62. PMCID: PMC165556 ParaDB: a tool for paralogy mapping in vertebrate genomes Magalie Leveugle, Karine Prat, Nadine Perrier, Daniel Birnbaum, and François Coulier Nucleic Acids Res. 2003 January 1; 31(1): 63–67. PMCID: PMC165553 ArrayExpress—a public repository for microarray gene expression data at the EBI Alvis Brazma, Helen Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Jaak Vilo, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Philippe Rocca-Serra, and Susanna-Assunta Sansone Nucleic Acids Res. 2003 January 1; 31(1): 68–71. PMCID: PMC165538 MEPD: a Medaka gene expression pattern database Thorsten Henrich, Mirana Ramialison, Rebecca Quiring, Beate Wittbrodt, Makoto Furutani-Seiki, Joachim Wittbrodt, and Hisato Kondoh Nucleic Acids Res. 2003 January 1; 31(1): 72–74. PMCID: PMC165464 An improved version of the DNA methylation database (MethDB) Céline Amoreira, Winfried Hindermann, and Christoph Grunau Nucleic Acids Res. 2003 January 1; 31(1): 75–77. PMCID: PMC165540 MTID: a database of Sleeping Beauty transposon insertions in mice Kevin Roberg-Perez, Corey M. Carlson, and David A. Largaespada Nucleic Acids Res. 2003 January 1; 31(1): 78–81. PMCID: PMC165492 NetAffx: Affymetrix probesets and annotations Guoying Liu, Ann E. Loraine, Ron Shigeta, Melissa Cline, Jill Cheng, Venu Valmeekam, Shaw Sun, David Kulp, and Michael A. Siani-Rose Nucleic Acids Res. 2003 January 1; 31(1): 82–86. PMCID: PMC165568 RECODE 2003 Pavel V. Baranov, Olga L. Gurvich, Andrew W. Hammer, Raymond F. Gesteland, and John F. Atkins Nucleic Acids Res. 2003 January 1; 31(1): 87–89. PMCID: PMC165471 The Arabidopsis SeedGenes Project Iris Tzafrir, Allan Dickerman, Olga Brazhnik, Quoc Nguyen, John McElver, Catherine Frye, David Patton, and David Meinke Nucleic Acids Res. 2003 January 1; 31(1): 90–93. PMCID: PMC165475 The Stanford Microarray Database: data access and quality assessment tools Jeremy Gollub, Catherine A. Ball, Gail Binkley, Janos Demeter, David B. Finkelstein, Joan M. Hebert, Tina Hernandez-Boussard, Heng Jin, Miroslava Kaloper, John C. Matese, Mark Schroeder, Patrick O. Brown, David Botstein, and Gavin Sherlock Nucleic Acids Res. 2003 January 1; 31(1): 94–96. PMCID: PMC165525 TRANSPATH®: an integrated database on signal transduction and a tool for array analysis Mathias Krull, Nico Voss, Claudia Choi, Susanne Pistor, Anatolij Potapov, and Edgar Wingender Nucleic Acids Res. 2003 January 1; 31(1): 97–100. PMCID: PMC165536 ASAP: the Alternative Splicing Annotation Project Christopher Lee, Levan Atanelov, Barmak Modrek, and Yi Xing Nucleic Acids Res. 2003 January 1; 31(1): 101–105. PMCID: PMC165476 MICdb: database of prokaryotic microsatellites Vattipally B. Sreenu, Vishwanath Alevoor, Javaregowda Nagaraju, and Hampapathalu A. Nagarajaram Nucleic Acids Res. 2003 January 1; 31(1): 106–108. PMCID: PMC165449 PACRAT: a database and analysis system for archaeal and bacterial intergenic sequence features William C. Ray and Charles J. Daniels Nucleic Acids Res. 2003 January 1; 31(1): 109–113. PMCID: PMC165460 PlantProm: a database of plant promoter sequences Ilham A. Shahmuradov, Alex J. Gammerman, John M. Hancock, Peter M. Bramley, and Victor V. Solovyev Nucleic Acids Res. 2003 January 1; 31(1): 114–117. PMCID: PMC165488 rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation Julia V. Ponomarenko, Tatyana I. Merkulova, Galina V. Orlova, Oleg N. Fokin, Elena V. Gorshkova, Anatoly S. Frolov, Vadim P. Valuev, and Mikhail P. Ponomarenko Nucleic Acids Res. 2003 January 1; 31(1): 118–121. PMCID: PMC165559 RTPrimerDB: the Real-Time PCR primer and probe database Filip Pattyn, Frank Speleman, Anne De Paepe, and Jo Vandesompele Nucleic Acids Res. 2003 January 1; 31(1): 122–123. PMCID: PMC165458 The SNP Consortium website: past, present and future Gudmundur A. Thorisson and Lincoln D. Stein Nucleic Acids Res. 2003 January 1; 31(1): 124–127. PMCID: PMC165499 Sputnik: a database platform for comparative plant genomics Stephen Rudd, Hans-Werner Mewes, and Klaus F.X. Mayer Nucleic Acids Res. 2003 January 1; 31(1): 128–132. PMCID: PMC165522 WormBase: a cross-species database for comparative genomics Todd W. Harris, Raymond Lee, Erich Schwarz, Keith Bradnam, Daniel Lawson, Wen Chen, Darin Blasier, Eimear Kenny, Fiona Cunningham, Ranjana Kishore, Juancarlos Chan, Hans-Michael Muller, Andrei Petcherski, Gudmundur Thorisson, Allen Day, Tamberlyn Bieri, Anthony Rogers, Chao-Kung Chen, John Spieth, Paul Sternberg, Richard Durbin, and Lincoln D. Stein Nucleic Acids Res. 2003 January 1; 31(1): 133–137. PMCID: PMC165500 The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa) Emmanuelle Karsenty, Emmanuel Barillot, Gwenola Tosser-Klopp, Yvette Lahbib-Mansais, Denis Milan, François Hatey, Susanna Cirera, Milena Sawera, Claus B. Jørgensen, Bhanu Chowdhary, Merete Fredholm, Klaus Wimmers, Siriluck Ponsuksili, Roberta Davoli, Luca Fontanesi, Silvia Braglia, Paolo Zambonelli, Daniele Bigi, Stefan Neuenschwander, and Joël Gellin Nucleic Acids Res. 2003 January 1; 31(1): 138–141. PMCID: PMC165508 Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE Marilyn Safran, Vered Chalifa-Caspi, Orit Shmueli, Tsviya Olender, Michal Lapidot, Naomi Rosen, Michael Shmoish, Yakov Peter, Gustavo Glusman, Ester Feldmesser, Avital Adato, Inga Peter, Miriam Khen, Tal Atarot, Yoram Groner, and Doron Lancet Nucleic Acids Res. 2003 January 1; 31(1): 142–146. PMCID: PMC165497 ASAP, a systematic annotation package for community analysis of genomes Jeremy D. Glasner, Paul Liss, Guy Plunkett, III, Aaron Darling, Tejasvini Prasad, Michael Rusch, Alexis Byrnes, Michael Gilson, Bryan Biehl, Frederick R. Blattner, and Nicole T. Perna Nucleic Acids Res. 2003 January 1; 31(1): 147–151. PMCID: PMC165572 BSD: the Biodegradative Strain Database John W. Urbance, James Cole, Paul Saxman, and James M. Tiedje Nucleic Acids Res. 2003 January 1; 31(1): 152–155. PMCID: PMC165479 CATMA: a complete Arabidopsis GST database Mark L. Crowe, Carine Serizet, Vincent Thareau, Sébastien Aubourg, Pierre Rouzé, Pierre Hilson, Jim Beynon, Peter Weisbeek, Paul van Hummelen, Philippe Reymond, Javier Paz-Ares, Wilfried Nietfeld, and Martin Trick Nucleic Acids Res. 2003 January 1; 31(1): 156–158. PMCID: PMC165518 CnidBase: The Cnidarian Evolutionary Genomics Database Joseph F. Ryan and John R. Finnerty Nucleic Acids Res. 2003 January 1; 31(1): 159–163. PMCID: PMC165563 The ERGOTM genome analysis and discovery system Ross Overbeek, Niels Larsen, Theresa Walunas, Mark D'Souza, Gordon Pusch, Eugene Selkov, Jr, Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vasieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, and Nikos Kyrpides Nucleic Acids Res. 2003 January 1; 31(1): 164–171. PMCID: PMC165577 The FlyBase database of the Drosophila genome projects and community literature Nucleic Acids Res. 2003 January 1; 31(1): 172–175. PMCID: PMC165541 GOBASE—a database of mitochondrial and chloroplast information Emmet A. O'Brien, Elarbi Badidi, Ania Barbasiewicz, Cristina deSousa, B. Franz Lang, and Gertraud Burger Nucleic Acids Res. 2003 January 1; 31(1): 176–178. PMCID: PMC165537 GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics Delphine Samson, Fabrice Legeai, Emmanuelle Karsenty, Sébastien Reboux, Jean-Baptiste Veyrieras, Jeremy Just, and Emmanuel Barillot Nucleic Acids Res. 2003 January 1; 31(1): 179–182. PMCID: PMC165507 GrainGenes, the genome database for small-grain crops David E. Matthews, Victoria L. Carollo, Gerard R. Lazo, and Olin D. Anderson Nucleic Acids Res. 2003 January 1; 31(1): 183–186. PMCID: PMC165505 HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes S. Garcia-Vallve, E. Guzman, M. A. Montero, and A. Romeu Nucleic Acids Res. 2003 January 1; 31(1): 187–189. PMCID: PMC165451 MOsDB: an integrated information resource for rice genomics Wojciech M. Karlowski, Heiko Schoof, Vijayalakshmi Janakiraman, Volker Stuempflen, and Klaus F. X. Mayer Nucleic Acids Res. 2003 January 1; 31(1): 190–192. PMCID: PMC165520 MGD: the Mouse Genome Database Judith A. Blake, Joel E. Richardson, Carol J. Bult, Jim A. Kadin, Janan T. Eppig, and The Mouse Genome Database Group Nucleic Acids Res. 2003 January 1; 31(1): 193–195. PMCID: PMC165494 MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome Anne-Françoise J. Lamblin, John A. Crow, James E. Johnson, Kevin A. T. Silverstein, Timothy M. Kunau, Alan Kilian, Diane Benz, Martina Stromvik, Gabriella Endré, Kathryn A. VandenBosch, Douglas R. Cook, Nevin D. Young, and Ernest F. Retzel Nucleic Acids Res. 2003 January 1; 31(1): 196–201. PMCID: PMC165566 OGRe: a relational database for comparative analysis of mitochondrial genomes Daniel Jameson, Andrew P. Gibson, Cendrine Hudelot, and Paul G. Higgs Nucleic Acids Res. 2003 January 1; 31(1): 202–206. PMCID: PMC165524 The PEDANT genome database Dmitrij Frishman, Martin Mokrejs, Denis Kosykh, Gabi Kastenmüller, Grigory Kolesov, Igor Zubrzycki, Christian Gruber, Birgitta Geier, Andreas Kaps, Kaj Albermann, Andreas Volz, Christian Wagner, Matthias Fellenberg, Klaus Heumann, and Hans-Werner Mewes Nucleic Acids Res. 2003 January 1; 31(1): 207–211. PMCID: PMC165452 PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data Amit Bahl, Brian Brunk, Jonathan Crabtree, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant, Hagai Ginsburg, Dinesh Gupta, Jessica C. Kissinger, Philip Labo, Li Li, Matthew D. Mailman, Arthur J. Milgram, David S. Pearson, David S. Roos, Jonathan Schug, Christian J. Stoeckert, Jr, and Patricia Whetzel Nucleic Acids Res. 2003 January 1; 31(1): 212–215. PMCID: PMC165528 Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins Shuai Weng, Qing Dong, Rama Balakrishnan, Karen Christie, Maria Costanzo, Kara Dolinski, Selina S. Dwight, Stacia Engel, Dianna G. Fisk, Eurie Hong, Laurie Issel-Tarver, Anand Sethuraman, Chandra Theesfeld, Rey Andrada, Gail Binkley, Christopher Lane, Mark Schroeder, David Botstein, and J. Michael Cherry Nucleic Acids Res. 2003 January 1; 31(1): 216–218. PMCID: PMC165501 SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data Maximilian Diehn, Gavin Sherlock, Gail Binkley, Heng Jin, John C. Matese, Tina Hernandez-Boussard, Christian A. Rees, J. Michael Cherry, David Botstein, Patrick O. Brown, and Ash A. Alizadeh Nucleic Acids Res. 2003 January 1; 31(1): 219–223. PMCID: PMC165461 The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community Seung Yon Rhee, William Beavis, Tanya Z. Berardini, Guanghong Chen, David Dixon, Aisling Doyle, Margarita Garcia-Hernandez, Eva Huala, Gabriel Lander, Mary Montoya, Neil Miller, Lukas A. Mueller, Suparna Mundodi, Leonore Reiser, Julie Tacklind, Dan C. Weems, Yihe Wu, Iris Xu, Daniel Yoo, Jungwon Yoon, and Peifen Zhang Nucleic Acids Res. 2003 January 1; 31(1): 224–228. PMCID: PMC165523 The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists Qiaoping Yuan, Shu Ouyang, Jia Liu, Bernard Suh, Foo Cheung, Razvan Sultana, Dan Lee, John Quackenbush, and C. Robin Buell Nucleic Acids Res. 2003 January 1; 31(1): 229–233. PMCID: PMC165506 ToxoDB: accessing the Toxoplasma gondii genome Jessica C. Kissinger, Bindu Gajria, Li Li, Ian T. Paulsen, and David S. Roos Nucleic Acids Res. 2003 January 1; 31(1): 234–236. PMCID: PMC165519 WorfDB: the Caenorhabditis elegans ORFeome Database Philippe Vaglio, Philippe Lamesch, Jérôme Reboul, Jean-François Rual, Monica Martinez, David Hill, and Marc Vidal Nucleic Acids Res. 2003 January 1; 31(1): 237–240. PMCID: PMC165539 The Zebrafish Information Network (ZFIN): the zebrafish model organism database Judy Sprague, Dave Clements, Tom Conlin, Pat Edwards, Ken Frazer, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, and Monte Westerfield Nucleic Acids Res. 2003 January 1; 31(1): 241–243. PMCID: PMC165474 ZmDB, an integrated database for maize genome research Qunfeng Dong, Laura Roy, Michael Freeling, Virginia Walbot, and Volker Brendel Nucleic Acids Res. 2003 January 1; 31(1): 244–247. PMCID: PMC165529 BIND: the Biomolecular Interaction Network Database Gary D. Bader, Doron Betel, and Christopher W. V. Hogue Nucleic Acids Res. 2003 January 1; 31(1): 248–250. PMCID: PMC165503 InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan, and Kui Lin Nucleic Acids Res. 2003 January 1; 31(1): 251–254. PMCID: PMC165526 KDBI: Kinetic Data of Bio-molecular Interactions database Z. L. Ji, X. Chen, C. J. Zhen, L. X. Yao, L. Y. Han, W. K. Yeo, P. C. Chung, H. S. Puy, Y. T. Tay, A. Muhammad, and Y. Z. Chen Nucleic Acids Res. 2003 January 1; 31(1): 255–257. PMCID: PMC165514 STRING: a database of predicted functional associations between proteins Christian von Mering, Martijn Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, and Berend Snel Nucleic Acids Res. 2003 January 1; 31(1): 258–261. PMCID: PMC165481 The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining Lynda B. M. Ellis, Bo Kyeng Hou, Wenjun Kang, and Lawrence P. Wackett Nucleic Acids Res. 2003 January 1; 31(1): 262–265. PMCID: PMC165495 PRODORIC: prokaryotic database of gene regulation Richard Münch, Karsten Hiller, Heiko Barg, Dana Heldt, Simone Linz, Edgar Wingender, and Dieter Jahn Nucleic Acids Res. 2003 January 1; 31(1): 266–269. PMCID: PMC165484 ALFRED: the ALelle FREquency Database. Update H. Rajeevan, M. V. Osier, K.-H. Cheung, H. Deng, L. Druskin, R. Heinzen, J. R. Kidd, S. Stein, A. J. Pakstis, N. P. Tosches, C.-C. Yeh, P. L. Miller, and K. K. Kidd Nucleic Acids Res. 2003 January 1; 31(1): 270–271. PMCID: PMC165490 Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003 Jean-Loup Huret, Philippe Dessen, and Alain Bernheim Nucleic Acids Res. 2003 January 1; 31(1): 272–274. PMCID: PMC165573 Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals Frank W. Nicholas Nucleic Acids Res. 2003 January 1; 31(1): 275–277. PMCID: PMC165521 BayGenomics: a resource of insertional mutations in mouse embryonic stem cells Doug Stryke, Michiko Kawamoto, Conrad C. Huang, Susan J. Johns, Leslie A. King, Courtney A. Harper, Elaine C. Meng, Roy E. Lee, Alice Yee, Larry L'Italien, Pao-Tien Chuang, Stephen G. Young, William C. Skarnes, Patricia C. Babbitt, and Thomas E. Ferrin Nucleic Acids Res. 2003 January 1; 31(1): 278–281. PMCID: PMC165511 INFEVERS: the Registry for FMF and hereditary inflammatory disorders mutations Cyril Sarrauste de Menthière, Stéphane Terrière, Denis Pugnère, Manuel Ruiz, Jacques Demaille, and Isabelle Touitou Nucleic Acids Res. 2003 January 1; 31(1): 282–285. PMCID: PMC165478 The MetaFMF website: a high quality tool for meta-analysis of FMF Denis Pugnère, Manuel Ruiz, Cyril Sarrauste de Menthière, Benjamin Masdoua, Jacques Demaille, and Isabelle Touitou Nucleic Acids Res. 2003 January 1; 31(1): 286–290. PMCID: PMC165544 PGDB: a curated and integrated database of genes related to the prostate Long-Cheng Li, Hong Zhao, Hiroaki Shiina, Christopher J. Kane, and Rajvir Dahiya Nucleic Acids Res. 2003 January 1; 31(1): 291–293. PMCID: PMC165455 GPCRDB information system for G protein-coupled receptors Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E. Cohen, and Gerrit Vriend Nucleic Acids Res. 2003 January 1; 31(1): 294–297. PMCID: PMC165550 Human immunodeficiency virus reverse transcriptase and protease sequence database Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, and Robert W. Shafer Nucleic Acids Res. 2003 January 1; 31(1): 298–303. PMCID: PMC165547 The Homeodomain Resource: 2003 update Sharmila Banerjee-Basu, Travis Moreland, Benjamin J. Hsu, Kenneth L. Trout, and Andreas D. Baxevanis Nucleic Acids Res. 2003 January 1; 31(1): 304–306. PMCID: PMC165565 IMGT, the international ImMunoGeneTics database® Marie-Paule Lefranc Nucleic Acids Res. 2003 January 1; 31(1): 307–310. PMCID: PMC165532 IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex James Robinson, Matthew J. Waller, Peter Parham, Natasja de Groot, Ronald Bontrop, Lorna J. Kennedy, Peter Stoehr, and Steven G. E. Marsh Nucleic Acids Res. 2003 January 1; 31(1): 311–314. PMCID: PMC165517 The InterPro Database, 2003 brings increased coverage and new features Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Phillip Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, and Evgueni M. Zdobnov Nucleic Acids Res. 2003 January 1; 31(1): 315–318. PMCID: PMC165493 The Lipase Engineering Database: a navigation and analysis tool for protein families Markus Fischer and Jürgen Pleiss Nucleic Acids Res. 2003 January 1; 31(1): 319–321. PMCID: PMC165462 MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion Marco Sardiello, Flavio Licciulli, Domenico Catalano, Marcella Attimonelli, and Corrado Caggese Nucleic Acids Res. 2003 January 1; 31(1): 322–324. PMCID: PMC165570 The Mitochondrial Protein Import Machinery of Plants (MPIMP) database Ryan Lister, Monika W. Murcha, and James Whelan Nucleic Acids Res. 2003 January 1; 31(1): 325–327. PMCID: PMC165502 The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome G. Dellaire, R. Farrall, and W.A. Bickmore Nucleic Acids Res. 2003 January 1; 31(1): 328–330. PMCID: PMC165465 NRMD: Nuclear Receptor Mutation Database Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, and Gert Vriend Nucleic Acids Res. 2003 January 1; 31(1): 331–333. PMCID: PMC165569 PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification Paul D. Thomas, Anish Kejariwal, Michael J. Campbell, Huaiyu Mi, Karen Diemer, Nan Guo, Istvan Ladunga, Betty Ulitsky-Lazareva, Anushya Muruganujan, Steven Rabkin, Jody A. Vandergriff, and Olivier Doremieux Nucleic Acids Res. 2003 January 1; 31(1): 334–341. PMCID: PMC165562 The PlantsP and PlantsT Functional Genomics Databases Jason H. Tchieu, Fariba Fana, J. Lynn Fink, Jeffrey Harper, T. Murlidharan Nair, R. Hannes Niedner, Douglas W. Smith, Kenneth Steube, Tobey M. Tam, Stella Veretnik, Degeng Wang, and Michael Gribskov Nucleic Acids Res. 2003 January 1; 31(1): 342–344. PMCID: PMC165472 The Protein Information Resource Cathy H. Wu, Lai-Su L. Yeh, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhangzhi Hu, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, C.R. Vinayaka, Jian Zhang, and Winona C. Barker Nucleic Acids Res. 2003 January 1; 31(1): 345–347. PMCID: PMC165487 ProtoNet: hierarchical classification of the protein space Ori Sasson, Avishay Vaaknin, Hillel Fleischer, Elon Portugaly, Yonatan Bilu, Nathan Linial, and Michal Linial Nucleic Acids Res. 2003 January 1; 31(1): 348–352. PMCID: PMC165543 RTKdb: database of receptor tyrosine kinase Julien Grassot, Guy Mouchiroud, and Guy Perrière Nucleic Acids Res. 2003 January 1; 31(1): 353–358. PMCID: PMC165483 SDAP: database and computational tools for allergenic proteins Ovidiu Ivanciuc, Catherine H. Schein, and Werner Braun Nucleic Acids Res. 2003 January 1; 31(1): 359–362. PMCID: PMC165457 SRPDB: Signal Recognition Particle Database Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, and Tore Samuelsson Nucleic Acids Res. 2003 January 1; 31(1): 363–364. PMCID: PMC165554 The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-Claude Blatter, Anne Estreicher, Elisabeth Gasteiger, Maria J. Martin, Karine Michoud, Claire O'Donovan, Isabelle Phan, Sandrine Pilbout, and Michel Schneider Nucleic Acids Res. 2003 January 1; 31(1): 365–370. PMCID: PMC165542 The TIGRFAMs database of protein families Daniel H. Haft, Jeremy D. Selengut, and Owen White Nucleic Acids Res. 2003 January 1; 31(1): 371–373. PMCID: PMC165575 TRANSFAC®: transcriptional regulation, from patterns to profiles V. Matys, E. Fricke, R. Geffers, E. Gößling, M. Haubrock, R. Hehl, K. Hornischer, D. Karas, A. E. Kel, O. V. Kel-Margoulis, D.-U. Kloos, S. Land, B. Lewicki-Potapov, H. Michael, R. Münch, I. Reuter, S. Rotert, H. Saxel, M. Scheer, S. Thiele, and E. Wingender Nucleic Acids Res. 2003 January 1; 31(1): 374–378. PMCID: PMC165555 Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences Angelo M. Facchiano, Antonio Facchiano, and Francesco Facchiano Nucleic Acids Res. 2003 January 1; 31(1): 379–382. PMCID: PMC165489 CDD: a curated Entrez database of conserved domain alignments Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Anna R. Panchenko, Bachoti S. Rao, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, and Stephen H. Bryant Nucleic Acids Res. 2003 January 1; 31(1): 383–387. PMCID: PMC165534 Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters E. V. Kriventseva, F. Servant, and R. Apweiler Nucleic Acids Res. 2003 January 1; 31(1): 388–389. PMCID: PMC165482 iProClass: an integrated database of protein family, function and structure information Hongzhan Huang, Winona C. Barker, Yongxing Chen, and Cathy H. Wu Nucleic Acids Res. 2003 January 1; 31(1): 390–392. PMCID: PMC165491 NESbase version 1.0: a database of nuclear export signals Tanja la Cour, Ramneek Gupta, Kristoffer Rapacki, Karen Skriver, Flemming M. Poulsen, and Søren Brunak Nucleic Acids Res. 2003 January 1; 31(1): 393–396. PMCID: PMC165548 NLSdb: database of nuclear localization signals Rajesh Nair, Phil Carter, and Burkhard Rost Nucleic Acids Res. 2003 January 1; 31(1): 397–399. PMCID: PMC165448 PRINTS and its automatic supplement, prePRINTS T. K. Attwood, P. Bradley, D. R. Flower, A. Gaulton, N. Maudling, A. L. Mitchell, G. Moulton, A. Nordle, K. Paine, P. Taylor, A. Uddin, and C. Zygouri Nucleic Acids Res. 2003 January 1; 31(1): 400–402. PMCID: PMC165477 The SBASE domain sequence library, release 10: domain architecture prediction Kristian Vlahoviček, Laszló Kaján, János Murvai, Zoltán Hegedűs, and Sándor Pongor Nucleic Acids Res. 2003 January 1; 31(1): 403–405. PMCID: PMC165545 TMPDB: a database of experimentally-characterized transmembrane topologies Masami Ikeda, Masafumi Arai, Toshikatsu Okuno, and Toshio Shimizu Nucleic Acids Res. 2003 January 1; 31(1): 406–409. PMCID: PMC165467 PEP: Predictions for Entire Proteomes Phil Carter, Jinfeng Liu, and Burkhard Rost Nucleic Acids Res. 2003 January 1; 31(1): 410–413. PMCID: PMC165549 The Proteome Analysis database: a tool for the in silico analysis of whole proteomes Manuela Pruess, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia Kriventseva, Virginie Mittard, Nicola Mulder, Isabelle Phan, Florence Servant, and Rolf Apweiler Nucleic Acids Res. 2003 January 1; 31(1): 414–417. PMCID: PMC165552 REBASE: restriction enzymes and methyltransferases Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis Nucleic Acids Res. 2003 January 1; 31(1): 418–420. PMCID: PMC165516 ARED 2.0: an update of AU-rich element mRNA database Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar Nucleic Acids Res. 2003 January 1; 31(1): 421–423. PMCID: PMC165470 Database for mobile group II introns Lixin Dai, Navtej Toor, Robert Olson, Andrew Keeping, and Steven Zimmerly Nucleic Acids Res. 2003 January 1; 31(1): 424–426. PMCID: PMC165496 IRESdb: the Internal Ribosome Entry Site database Sophie Bonnal, Christel Boutonnet, Leonel Prado-Lourenço, and Stéphan Vagner Nucleic Acids Res. 2003 January 1; 31(1): 427–428. PMCID: PMC165450 Noncoding regulatory RNAs database Maciej Szymański, Volker A. Erdmann, and Jan Barciszewski Nucleic Acids Res. 2003 January 1; 31(1): 429–431. PMCID: PMC165571 Plant snoRNA database John W. S. Brown, Manuel Echeverria, Liang-Hu Qu, Todd M. Lowe, Jean-Pierre Bachellerie, Alexander Hüttenhofer, James P. Kastenmayer, Pamela J. Green, Paul Shaw, and Dave F. Marshall Nucleic Acids Res. 2003 January 1; 31(1): 432–435. PMCID: PMC165456 PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes Guglielmo Rainaldi, Mariateresa Volpicella, Flavio Licciulli, Sabino Liuni, Raffaele Gallerani, and Luigi R. Ceci Nucleic Acids Res. 2003 January 1; 31(1): 436–438. PMCID: PMC165527 Rfam: an RNA family database Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, and Sean R. Eddy Nucleic Acids Res. 2003 January 1; 31(1): 439–441. PMCID: PMC165453 The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy J. R. Cole, B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje Nucleic Acids Res. 2003 January 1; 31(1): 442–443. PMCID: PMC165486 SubViral RNA: a database of the smallest known auto-replicable RNA species Martin Pelchat, Lynda Rocheleau, Jonathan Perreault, and Jean-Pierre Perreault Nucleic Acids Res. 2003 January 1; 31(1): 444–445. PMCID: PMC165473 tmRDB (tmRNA database) Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, and Jacek Wower Nucleic Acids Res. 2003 January 1; 31(1): 446–447. PMCID: PMC165466 CADB: Conformation Angles DataBase of proteins S. S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi, and K. Sekar Nucleic Acids Res. 2003 January 1; 31(1): 448–451. PMCID: PMC165531 The CATH database: an extended protein family resource for structural and functional genomics F. M. G. Pearl, C. F. Bennett, J. E. Bray, A. P. Harrison, N. Martin, A. Shepherd, I. Sillitoe, J. Thornton, and C. A. Orengo Nucleic Acids Res. 2003 January 1; 31(1): 452–455. PMCID: PMC165509 DSMM: a Database of Simulated Molecular Motions Giacomo Finocchiaro, Ting Wang, Rene Hoffmann, Aitor Gonzalez, and Rebecca C. Wade Nucleic Acids Res. 2003 January 1; 31(1): 456–457. PMCID: PMC165560 E-MSD: the European Bioinformatics Institute Macromolecular Structure Database H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel, P. McNeil, A. Naim, R. Newman, T. Oldfield, J. Pineda, A. Rachedi, J. Copeland, A. Sitnov, S. Sobhany, A. Suarez-Uruena, J. Swaminathan, M. Tagari, J. Tate, S. Tromm, S. Velankar, and W. Vranken Nucleic Acids Res. 2003 January 1; 31(1): 458–462. PMCID: PMC165512 Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species Akihiro Yamaguchi, Mitsuo Iwadate, Ei-ichiro Suzuki, Kei Yura, Shigetsugu Kawakita, Hideaki Umeyama, and Mitiko Go Nucleic Acids Res. 2003 January 1; 31(1): 463–468. PMCID: PMC165564 Gene3D: structural assignments for the biologist and bioinformaticist alike Daniel W. A. Buchan, Stuart C. G. Rison, James E. Bray, David Lee, Frances Pearl, Janet M. Thornton, and Christine A. Orengo Nucleic Acids Res. 2003 January 1; 31(1): 469–473. PMCID: PMC165498 MMDB: Entrez's 3D-structure database Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, and Stephen H. Bryant Nucleic Acids Res. 2003 January 1; 31(1): 474–477. PMCID: PMC165533 MolMovDB: analysis and visualization of conformational change and structural flexibility Nathaniel Echols, Duncan Milburn, and Mark Gerstein Nucleic Acids Res. 2003 January 1; 31(1): 478–482. PMCID: PMC165551 NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0 Wing Lok Abe Kurtz Chiu, Chun Ngai Sze, Nap Tak Ma, Lai Fan Chiu, Chung Wai Leung, and Steve Chik Fun Au-Yeung Nucleic Acids Res. 2003 January 1; 31(1): 483–485. PMCID: PMC165561 Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database V. S. Gowri, Shashi B. Pandit, P. S. Karthik, N. Srinivasan, and S. Balaji Nucleic Acids Res. 2003 January 1; 31(1): 486–488. PMCID: PMC165510 The Protein Data Bank and structural genomics John Westbrook, Zukang Feng, Li Chen, Huanwang Yang, and Helen M. Berman Nucleic Acids Res. 2003 January 1; 31(1): 489–491. PMCID: PMC165515 PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003 Tamotsu Noguchi and Yutaka Akiyama Nucleic Acids Res. 2003 January 1; 31(1): 492–493. PMCID: PMC165469 The PSSH database of alignments between protein sequences and tertiary structures Andrea Schafferhans, Joachim E. W. Meyer, and Seán I. O'Donoghue Nucleic Acids Res. 2003 January 1; 31(1): 494–498. PMCID: PMC165557 The RESID Database of Protein Modifications: 2003 developments John S. Garavelli Nucleic Acids Res. 2003 January 1; 31(1): 499–501. PMCID: PMC165485 RNABase: an annotated database of RNA structures Venkatesh L. Murthy and George D. Rose Nucleic Acids Res. 2003 January 1; 31(1): 502–504. PMCID: PMC165459 The Structure Superposition Database Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, and Patricia C. Babbitt Nucleic Acids Res. 2003 January 1; 31(1): 505–510. PMCID: PMC165574 GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update Catherine A. Cooper, Hiren J. Joshi, Mathew J. Harrison, Marc R. Wilkins, and Nicolle H. Packer Nucleic Acids Res. 2003 January 1; 31(1): 511–513. PMCID: PMC165546 probeBase: an online resource for rRNA-targeted oligonucleotide probes Alexander Loy, Matthias Horn, and Michael Wagner Nucleic Acids Res. 2003 January 1; 31(1): 514–516. PMCID: PMC165463 |