Databases in Molecular Biology (2003):

An overview about molecular biological databases is given each year in the January issue of Nucleic Acids Research. The published articles are very useful to get fast and qualified answers to related questions. Please enjoy the list of articles published in January 2003:

• Andreas D. Baxevanis
  The Molecular Biology Database Collection: 2003 update
  Nucleic Acids Res. 31: 1-12. Database Listing

• S. Miyazaki, H. Sugawara, T. Gojobori, and Y. Tateno
  DNA Data Bank of Japan (DDBJ) in XML
  Nucleic Acids Res. 31: 13-16.

• 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
  The EMBL Nucleotide Sequence Database: major new developments
  Nucleic Acids Res. 31: 17-22.

• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
  GenBank
  Nucleic Acids Res. 31: 23-27.

• 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
  Database resources of the National Center for Biotechnology
  Nucleic Acids Res. 31: 28-33.

• Kim D. Pruitt, Tatiana Tatusova, and Donna R. Maglott
  NCBI Reference Sequence Project: update and current status
  Nucleic Acids Res. 31: 34-37.

• 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
  Ensembl 2002: accommodating comparative genomics
  Nucleic Acids Res. 31: 38-42.

• 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
  The European Bioinformatics Institute's data resources
  Nucleic Acids Res. 31: 43-50.

• 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
  The UCSC Genome Browser Database
  Nucleic Acids Res. 31: 51-54.

• C. Dieterich, H. Wang, K. Rateitschak, H. Luz, and M. Vingron
  CORG: a database for COmparative Regulatory Genomics
  Nucleic Acids Res. 31: 55-57.

• Ikuo Uchiyama
  MBGD: microbial genome database for comparative analysis
  Nucleic Acids Res. 31: 58-62.

• Magalie Leveugle, Karine Prat, Nadine Perrier, Daniel Birnbaum, and Fran�ois Coulier
  ParaDB: a tool for paralogy mapping in vertebrate genomes
  Nucleic Acids Res. 31: 63-67.

• 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
  ArrayExpress - a public repository for microarray gene expression data at the EBI
  Nucleic Acids Res. 31: 68-71.

• Thorsten Henrich, Mirana Ramialison, Rebecca Quiring, Beate Wittbrodt, Makoto Furutani-Seiki, Joachim Wittbrodt, and Hisato Kondoh
  MEPD: a Medaka gene expression pattern database
  Nucleic Acids Res. 31: 72-74.

• CŽline Amoreira, Winfried Hindermann, and Christoph Grunau
  An improved version of the DNA methylation database (MethDB)
  Nucleic Acids Res. 31: 75-77.

• Kevin Roberg-Perez, Corey M. Carlson, and David A. Largaespada
  MTID: a database of Sleeping Beauty transposon insertions in mice
  Nucleic Acids Res. 31: 78-81.

• Guoying Liu, Ann E. Loraine, Ron Shigeta, Melissa Cline, Jill Cheng, Venu Valmeekam, Shaw Sun, David Kulp, and Michael A. Siani-Rose
  NetAffx: Affymetrix probesets and annotations
  Nucleic Acids Res. 31: 82-86.

• Pavel V. Baranov, Olga L. Gurvich, Andrew W. Hammer, Raymond F. Gesteland, and John F. Atkins
  RECODE 2003
  Nucleic Acids Res. 31: 87-89.

• Iris Tzafrir, Allan Dickerman, Olga Brazhnik, Quoc Nguyen, John McElver, Catherine Frye, David Patton, and David Meinke
  The Arabidopsis SeedGenes Project
  Nucleic Acids Res. 31: 90-93.

• 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
  The Stanford Microarray Database: data access and quality assessment tools
  Nucleic Acids Res. 31: 94-96.

• Mathias Krull, Nico Voss, Claudia Choi, Susanne Pistor, Anatolij Potapov, and Edgar Wingender
  TRANSPATH^¨: an integrated database on signal transduction and a tool for array analysis
  Nucleic Acids Res. 31: 97-100.

• Christopher Lee, Levan Atanelov, Barmak Modrek, and Yi Xing
  ASAP: the Alternative Splicing Annotation Project
  Nucleic Acids Res. 31: 101-105.

• Vattipally B. Sreenu, Vishwanath Alevoor, Javaregowda Nagaraju, and Hampapathalu A. Nagarajaram
  MICdb: database of prokaryotic microsatellites
  Nucleic Acids Res. 31: 106-108.

• William C. Ray and Charles J. Daniels
  PACRAT: a database and analysis system for archaeal and bacterial intergenic sequence features
  Nucleic Acids Res. 31: 109-113.

• Ilham A. Shahmuradov, Alex J. Gammerman, John M. Hancock, Peter M. Bramley, and Victor V. Solovyev
  PlantProm: a database of plant promoter sequences
  Nucleic Acids Res. 31: 114-117.

• 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
  rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation
  Nucleic Acids Res. 31: 118-121.

• Filip Pattyn, Frank Speleman, Anne De Paepe, and Jo Vandesompele
  RTPrimerDB: the Real-Time PCR primer and probe database
  Nucleic Acids Res. 31: 122-123.

• Gudmundur A. Thorisson and Lincoln D. Stein
  The SNP Consortium website: past, present and future
  Nucleic Acids Res. 31: 124-127.

• Stephen Rudd, Hans-Werner Mewes, and Klaus F.X. Mayer
  Sputnik: a database platform for comparative plant genomics
  Nucleic Acids Res. 31: 128-132.

• 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
  WormBase: a cross-species database for comparative genomics
  Nucleic Acids Res. 31: 133-137.

• Emmanuelle Karsenty, Emmanuel Barillot, Gwenola Tosser-Klopp, Yvette Lahbib-Mansais, Denis Milan, Fran�ois Hatey, Susanna Cirera, Milena Sawera, Claus B. J¿rgensen, Bhanu Chowdhary, Merete Fredholm, Klaus Wimmers, Siriluck Ponsuksili, Roberta Davoli, Luca Fontanesi, Silvia Braglia, Paolo Zambonelli, Daniele Bigi, Stefan Neuenschwander, and Jo‘l Gellin
  The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa)
  Nucleic Acids Res. 31: 138-141.

• 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
  Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE
  Nucleic Acids Res. 31: 142-146.

• 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
  ASAP, a systematic annotation package for community analysis of genomes
  Nucleic Acids Res. 31: 147-151.

• John W. Urbance, James Cole, Paul Saxman, and James M. Tiedje
  BSD: the Biodegradative Strain Database
  Nucleic Acids Res. 31: 152-155.

• Mark L. Crowe, Carine Serizet, Vincent Thareau, SŽbastien Aubourg, Pierre RouzŽ, Pierre Hilson, Jim Beynon, Peter Weisbeek, Paul van Hummelen, Philippe Reymond, Javier Paz-Ares, Wilfried Nietfeld, and Martin Trick
  CATMA: a complete Arabidopsis GST database
  Nucleic Acids Res. 31: 156-158.

• Joseph F. Ryan and John R. Finnerty
  CnidBase: The Cnidarian Evolutionary Genomics Database
  Nucleic Acids Res. 31: 159-163.

• 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
  The ERGO^TM genome analysis and discovery system
  Nucleic Acids Res. 31: 164-171.

• The FlyBase Consortium
  The FlyBase database of the Drosophila genome projects and community literature
  Nucleic Acids Res. 31: 172-175.

• Emmet A. O'Brien, Elarbi Badidi, Ania Barbasiewicz, Cristina deSousa, B. Franz Lang, and Gertraud Burger
  GOBASE - a database of mitochondrial and chloroplast information
  Nucleic Acids Res. 31: 176-178.

• Delphine Samson, Fabrice Legeai, Emmanuelle Karsenty, SŽbastien Reboux, Jean-Baptiste Veyrieras, Jeremy Just, and Emmanuel Barillot
  GŽnoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics
  Nucleic Acids Res. 31: 179-182.

• David E. Matthews, Victoria L. Carollo, Gerard R. Lazo, and Olin D. Anderson
  GrainGenes, the genome database for small-grain crops
  Nucleic Acids Res. 31: 183-186.
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• S. Garcia-Vallve, E. Guzman, M. A. Montero, and A. Romeu
  HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes
  Nucleic Acids Res. 31: 187-189.

• Wojciech M. Karlowski, Heiko Schoof, Vijayalakshmi Janakiraman, Volker Stuempflen, and Klaus F. X. Mayer
  MOsDB: an integrated information resource for rice genomics
  Nucleic Acids Res. 31: 190-192.

• Judith A. Blake, Joel E. Richardson, Carol J. Bult, Jim A. Kadin, and Janan T. Eppig
  MGD: the Mouse Genome Database
  Nucleic Acids Res. 31: 193-195.
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• Anne-Fran�oise J. Lamblin, John A. Crow, James E. Johnson, Kevin A. T. Silverstein, Timothy M. Kunau, Alan Kilian, Diane Benz, Martina Stromvik, Gabriella EndrŽ, Kathryn A. VandenBosch, Douglas R. Cook, Nevin D. Young, and Ernest F. Retzel
  MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome
  Nucleic Acids Res. 31: 196-201.

• Daniel Jameson, Andrew P. Gibson, Cendrine Hudelot, and Paul G. Higgs
  OGRe: a relational database for comparative analysis of mitochondrial genomes
  Nucleic Acids Res. 31: 202-206.

• Dmitrij Frishman, Martin Mokrejs, Denis Kosykh, Gabi KastenmŸller, Grigory Kolesov, Igor Zubrzycki, Christian Gruber, Birgitta Geier, Andreas Kaps, Kaj Albermann, Andreas Volz, Christian Wagner, Matthias Fellenberg, Klaus Heumann, and Hans-Werner Mewes
  The PEDANT genome database
  Nucleic Acids Res. 31: 207-211.

• 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
  PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
  Nucleic Acids Res. 31: 212-215.

• 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
  Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins
  Nucleic Acids Res. 31: 216-218.

• 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
  SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
  Nucleic Acids Res. 31: 219-223.

• 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
  The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
  Nucleic Acids Res. 31: 224-228.

• Qiaoping Yuan, Shu Ouyang, Jia Liu, Bernard Suh, Foo Cheung, Razvan Sultana, Dan Lee, John Quackenbush, and C. Robin Buell
  The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists
  Nucleic Acids Res. 31: 229-233.

• Jessica C. Kissinger, Bindu Gajria, Li Li, Ian T. Paulsen, and David S. Roos
  ToxoDB: accessing the Toxoplasma gondii genome
  Nucleic Acids Res. 31: 234-236.

• Philippe Vaglio, Philippe Lamesch, JŽr™me Reboul, Jean-Fran�ois Rual, Monica Martinez, David Hill, and Marc Vidal
  WorfDB: the Caenorhabditis elegans ORFeome Database
  Nucleic Acids Res. 31: 237-240.

• Judy Sprague, Dave Clements, Tom Conlin, Pat Edwards, Ken Frazer, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, and Monte Westerfield
  The Zebrafish Information Network (ZFIN): the zebrafish model organism database
  Nucleic Acids Res. 31: 241-243.

• Qunfeng Dong, Laura Roy, Michael Freeling, Virginia Walbot, and Volker Brendel
  ZmDB, an integrated database for maize genome research
  Nucleic Acids Res. 31: 244-247.

• Gary D. Bader, Doron Betel, and Christopher W. V. Hogue
  BIND: the Biomolecular Interaction Network Database
  Nucleic Acids Res. 31: 248-250.
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• See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan, and Kui Lin
  InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes
  Nucleic Acids Res. 31: 251-254.

• 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
  KDBI: Kinetic Data of Bio-molecular Interactions database
  Nucleic Acids Res. 31: 255-257.

• Christian von Mering, Martijn Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, and Berend Snel
  STRING: a database of predicted functional associations between proteins
  Nucleic Acids Res. 31: 258-261.

• Lynda B. M. Ellis, Bo Kyeng Hou, Wenjun Kang, and Lawrence P. Wackett
  The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining
  Nucleic Acids Res. 31: 262-265.

• Richard MŸnch, Karsten Hiller, Heiko Barg, Dana Heldt, Simone Linz, Edgar Wingender, and Dieter Jahn
  PRODORIC: prokaryotic database of gene regulation
  Nucleic Acids Res. 31: 266-269.

• 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
  ALFRED: the ALelle FREquency Database. Update
  Nucleic Acids Res. 31: 270-271.

• Jean-Loup Huret, Philippe Dessen, and Alain Bernheim
  Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003
  Nucleic Acids Res. 31: 272-274.

• Frank W. Nicholas
  Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals
  Nucleic Acids Res. 31: 275-277.

• 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
  BayGenomics: a resource of insertional mutations in mouse embryonic stem cells
  Nucleic Acids Res. 31: 278-281.

• Cyril Sarrauste de Menthi�re, StŽphane Terri�re, Denis Pugn�re, Manuel Ruiz, Jacques Demaille, and Isabelle Touitou
  INFEVERS: the Registry for FMF and hereditary inflammatory disorders mutations
  Nucleic Acids Res. 31: 282-285.

• Denis Pugn�re, Manuel Ruiz, Cyril Sarrauste de Menthi�re, Benjamin Masdoua, Jacques Demaille, and Isabelle Touitou
  The MetaFMF website: a high quality tool for meta-analysis of FMF
  Nucleic Acids Res. 31: 286-290.

• Long-Cheng Li, Hong Zhao, Hiroaki Shiina, Christopher J. Kane, and Rajvir Dahiya
  PGDB: a curated and integrated database of genes related to the prostate
  Nucleic Acids Res. 31: 291-293.

• Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E. Cohen, and Gerrit Vriend
  GPCRDB information system for G protein-coupled receptors
  Nucleic Acids Res. 31: 294-297.

• Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, and Robert W. Shafer
  Human immunodeficiency virus reverse transcriptase and protease sequence database
  Nucleic Acids Res. 31: 298-303.

• Sharmila Banerjee-Basu, Travis Moreland, Benjamin J. Hsu, Kenneth L. Trout, and Andreas D. Baxevanis
  The Homeodomain Resource: 2003 update
  Nucleic Acids Res. 31: 304-306.

• Marie-Paule Lefranc
  IMGT, the international ImMunoGeneTics database^¨
  Nucleic Acids Res. 31: 307-310.

• James Robinson, Matthew J. Waller, Peter Parham, Natasja de Groot, Ronald Bontrop, Lorna J. Kennedy, Peter Stoehr, and Steven G. E. Marsh
  IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex
  Nucleic Acids Res. 31: 311-314.

• 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
  The InterPro Database, 2003 brings increased coverage and new features
  Nucleic Acids Res. 31: 315-318.
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• Markus Fischer and JŸrgen Pleiss
  The Lipase Engineering Database: a navigation and analysis tool for protein families
  Nucleic Acids Res. 31: 319-321.

• Marco Sardiello, Flavio Licciulli, Domenico Catalano, Marcella Attimonelli, and Corrado Caggese
  MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion
  Nucleic Acids Res. 31: 322-324.

• Ryan Lister, Monika W. Murcha, and James Whelan
  The Mitochondrial Protein Import Machinery of Plants (MPIMP) database
  Nucleic Acids Res. 31: 325-327.

• G. Dellaire, R. Farrall, and W.A. Bickmore
  The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome
  Nucleic Acids Res. 31: 328-330.

• Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, and Gert Vriend
  NRMD: Nuclear Receptor Mutation Database
  Nucleic Acids Res. 31: 331-333.

• 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
  PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification
  Nucleic Acids Res. 31: 334-341.

• 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
  The PlantsP and PlantsT Functional Genomics Databases
  Nucleic Acids Res. 31: 342-344.

• 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
  The Protein Information Resource
  Nucleic Acids Res. 31: 345-347.

• Ori Sasson, Avishay Vaaknin, Hillel Fleischer, Elon Portugaly, Yonatan Bilu, Nathan Linial, and Michal Linial
  ProtoNet: hierarchical classification of the protein space
  Nucleic Acids Res. 31: 348-352.

• Julien Grassot, Guy Mouchiroud, and Guy Perri�re
  RTKdb: database of receptor tyrosine kinase
  Nucleic Acids Res. 31: 353-358.

• Ovidiu Ivanciuc, Catherine H. Schein, and Werner Braun
  SDAP: database and computational tools for allergenic proteins
  Nucleic Acids Res. 31: 359-362.

• Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, and Tore Samuelsson
  SRPDB: Signal Recognition Particle Database
  Nucleic Acids Res. 31: 363-364.

• 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
  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
  Nucleic Acids Res. 31: 365-370.

• Daniel H. Haft, Jeremy D. Selengut, and Owen White
  The TIGRFAMs database of protein families
  Nucleic Acids Res. 31: 371-373.

• V. Matys, E. Fricke, R. Geffers, E. Gš§ling, 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. MŸnch, I. Reuter, S. Rotert, H. Saxel, M. Scheer, S. Thiele, and E. Wingender
  TRANSFAC^¨: transcriptional regulation, from patterns to profiles
  Nucleic Acids Res. 31: 374-378.

• Angelo M. Facchiano, Antonio Facchiano, and Francesco Facchiano
  Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences
  Nucleic Acids Res. 31: 379-382.

• 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
  CDD: a curated Entrez database of conserved domain alignments
  Nucleic Acids Res. 31: 383-387.

• E. V. Kriventseva, F. Servant, and R. Apweiler
  Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters
  Nucleic Acids Res. 31: 388-389.

• Hongzhan Huang, Winona C. Barker, Yongxing Chen, and Cathy H. Wu
  iProClass: an integrated database of protein family, function and structure information
  Nucleic Acids Res. 31: 390-392.

• Tanja la Cour, Ramneek Gupta, Kristoffer Rapacki, Karen Skriver, Flemming M. Poulsen, and S¿ren Brunak
  NESbase version 1.0: a database of nuclear export signals
  Nucleic Acids Res. 31: 393-396.

• Rajesh Nair, Phil Carter, and Burkhard Rost
  NLSdb: database of nuclear localization signals
  Nucleic Acids Res. 31: 397-399.

• 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
  PRINTS and its automatic supplement, prePRINTS
  Nucleic Acids Res. 31: 400-402.

• Kristian Vlahovicek, Laszl— Kaj‡n, J‡nos Murvai, Zolt‡n Hegeds, and S‡ndor Pongor
  The SBASE domain sequence library, release 10: domain architecture prediction
  Nucleic Acids Res. 31: 403-405.

• Masami Ikeda, Masafumi Arai, Toshikatsu Okuno, and Toshio Shimizu
  TMPDB: a database of experimentally-characterized transmembrane topologies
  Nucleic Acids Res. 31: 406-409.

• Phil Carter, Jinfeng Liu, and Burkhard Rost
  PEP: Predictions for Entire Proteomes
  Nucleic Acids Res. 31: 410-413.

• Manuela Pruess, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia Kriventseva, Virginie Mittard, Nicola Mulder, Isabelle Phan, Florence Servant, and Rolf Apweiler
  The Proteome Analysis database: a tool for the in silico analysis of whole proteomes
  Nucleic Acids Res. 31: 414-417.

• Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis
  REBASE: restriction enzymes and methyltransferases
  Nucleic Acids Res. 31: 418-420.

• Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar
  ARED 2.0: an update of AU-rich element mRNA database
  Nucleic Acids Res. 31: 421-423.

• Lixin Dai, Navtej Toor, Robert Olson, Andrew Keeping, and Steven Zimmerly
  Database for mobile group II introns
  Nucleic Acids Res. 31: 424-426.

• Sophie Bonnal, Christel Boutonnet, Leonel Prado-Louren�o, and StŽphan Vagner
  IRESdb: the Internal Ribosome Entry Site database
  Nucleic Acids Res. 31: 427-428.

• Maciej Szymanski, Volker A. Erdmann, and Jan Barciszewski
  Noncoding regulatory RNAs database
  Nucleic Acids Res. 31: 429-431.

• John W. S. Brown, Manuel Echeverria, Liang-Hu Qu, Todd M. Lowe, Jean-Pierre Bachellerie, Alexander HŸttenhofer, James P. Kastenmayer, Pamela J. Green, Paul Shaw, and Dave F. Marshall
  Plant snoRNA database
  Nucleic Acids Res. 31: 432-435.
  Ê

• Guglielmo Rainaldi, Mariateresa Volpicella, Flavio Licciulli, Sabino Liuni, Raffaele Gallerani, and Luigi R. Ceci
  PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes
  Nucleic Acids Res. 31: 436-438.
  Ê

• Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, and Sean R. Eddy
  Rfam: an RNA family database
  Nucleic Acids Res. 31: 439-441.

• 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
  The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
  Nucleic Acids Res. 31: 442-443.

• Martin Pelchat, Lynda Rocheleau, Jonathan Perreault, and Jean-Pierre Perreault
  SubViral RNA: a database of the smallest known auto-replicable RNA species
  Nucleic Acids Res. 31: 444-445.

• Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, and Jacek Wower
  tmRDB (tmRNA database)
  Nucleic Acids Res. 31: 446-447.

• S. S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi, and K. Sekar
  CADB: Conformation Angles DataBase of proteins
  Nucleic Acids Res. 31: 448-451.

• 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
  The CATH database: an extended protein family resource for structural and functional genomics
  Nucleic Acids Res. 31: 452-455.

• Giacomo Finocchiaro, Ting Wang, Rene Hoffmann, Aitor Gonzalez, and Rebecca C. Wade
  DSMM: a Database of Simulated Molecular Motions
  Nucleic Acids Res. 31: 456-457.

• 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
  E-MSD: the European Bioinformatics Institute Macromolecular Structure Database
  Nucleic Acids Res. 31: 458-462.

• Akihiro Yamaguchi, Mitsuo Iwadate, Ei-ichiro Suzuki, Kei Yura, Shigetsugu Kawakita, Hideaki Umeyama, and Mitiko Go
  Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species
  Nucleic Acids Res. 31: 463-468.

• Daniel W. A. Buchan, Stuart C. G. Rison, James E. Bray, David Lee, Frances Pearl, Janet M. Thornton, and Christine A. Orengo
  Gene3D: structural assignments for the biologist and bioinformaticist alike
  Nucleic Acids Res. 31: 469-473.

• 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
  MMDB: Entrez's 3D-structure database
  Nucleic Acids Res. 31: 474-477.

• Nathaniel Echols, Duncan Milburn, and Mark Gerstein
  MolMovDB: analysis and visualization of conformational change and structural flexibility
  Nucleic Acids Res. 31: 478-482.

• Wing Lok Abe Kurtz Chiu, Chun Ngai Sze, Nap Tak Ma, Lai Fan Chiu, Chung Wai Leung, and Steve Chik Fun Au-Yeung
  NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0
  Nucleic Acids Res. 31: 483-485.

• V. S. Gowri, Shashi B. Pandit, P. S. Karthik, N. Srinivasan, and S. Balaji
  Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database
  Nucleic Acids Res. 31: 486-488.

• John Westbrook, Zukang Feng, Li Chen, Huanwang Yang, and Helen M. Berman
  The Protein Data Bank and structural genomics
  Nucleic Acids Res. 31: 489-491.

• Tamotsu Noguchi and Yutaka Akiyama
  PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
  Nucleic Acids Res. 31: 492-493.

• Andrea Schafferhans, Joachim E. W. Meyer, and Se‡n I. O'Donoghue
  The PSSH database of alignments between protein sequences and tertiary structures
  Nucleic Acids Res. 31: 494-498.

• John S. Garavelli
  The RESID Database of Protein Modifications: 2003 developments
  Nucleic Acids Res. 31: 499-501.

• Venkatesh L. Murthy and George D. Rose
  RNABase: an annotated database of RNA structures
  Nucleic Acids Res. 31: 502-504.

• Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, and Patricia C. Babbitt
  The Structure Superposition Database
  Nucleic Acids Res. 31: 505-510.

• Catherine A. Cooper, Hiren J. Joshi, Mathew J. Harrison, Marc R. Wilkins, and Nicolle H. Packer
  GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update
  Nucleic Acids Res. 31: 511-513.

• Alexander Loy, Matthias Horn, and Michael Wagner
  probeBase: an online resource for rRNA-targeted oligonucleotide probes
  Nucleic Acids Res. 31: 514-516.

>Latest update: April 10, 2003

Ralf Koebnik
Institut de recherche pour le dèveloppement
UMR 5096, CNRS-UP-IRD
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