Databases in Molecular Biology (2004):

An overview about molecular biological databases is given each year in a special issue (January) 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 2004:

• Michael Y. Galperin
  The Molecular Biology Database Collection: 2004 update
  Nucleic Acids Res. 32: D3-D22. Database Listing

• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
  GenBank: update
  Nucleic Acids Res. 32: D23-D26.

• Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Maria Garcia-Pastor, Nicola Harte, Carola Kanz, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Peter Stoehr, Guenter Stoesser, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler
  The EMBL Nucleotide Sequence Database
  Nucleic Acids Res. 32: D27-D30.

• S. Miyazaki, H. Sugawara, K. Ikeo, T. Gojobori, and Y. Tateno
  DDBJ in the stream of various biological data
  Nucleic Acids Res. 32: D31-D34.

• David L. Wheeler, Deanna M. Church, Ron Edgar, Scott Federhen, Wolfgang Helmberg, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tugba O. Suzek, Tatiana A. Tatusova, and Lukas Wagner
  Database resources of the National Center for Biotechnology Information: update
  Nucleic Acids Res. 32: D35-D40.

• H. W. Mewes, C. Amid, R. Arnold, D. Frishman, U. Güldener, G. Mannhaupt, M. Münsterkötter, P. Pagel, N. Strack, V. Stümpflen, J. Warfsmann, and A. Ruepp
  MIPS: analysis and annotation of proteins from whole genomes
  Nucleic Acids Res. 32: D41-D44.

• Raphaël Leplae, Aline Hebrant, Shoshana J. Wodak, and Ariane Toussaint
  ACLAME: A CLAssification of Mobile genetic Elements
  Nucleic Acids Res. 32: D45-D49.

• Jan Paces, Adam Pavlícek, Radek Zika, Vladimir V. Kapitonov, Jerzy Jurka, and Václav Paces
  HERVd: the Human Endogenous RetroViruses Database: update
  Nucleic Acids Res. 32: D50.

• Thierry-Pascal Baum, Nicolas Pasqual, Florence Thuderoz, Vivien Hierle, Denys Chaume, Marie-Paule Lefranc, Evelyne Jouvin-Marche, Patrice-Noël Marche, and Jacques Demongeot
  IMGT/GeneInfo: enhancing V(D)J recombination database accessibility
  Nucleic Acids Res. 32: D51-D54.

• Yogita Mantri and Kelly P. Williams
  Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
  Nucleic Acids Res. 32: D55-D58.

• Vivek Gopalan, Tin Wee Tan, Bernett T. K. Lee, and Shoba Ranganathan
  Xpro: database of eukaryotic protein-encoding genes
  Nucleic Acids Res. 32: D59-D63.

• T. A. Thanaraj, Stefan Stamm, Francis Clark, Jean-Jack Riethoven, Vincent Le Texier, and Juha Muilu
  ASD: the Alternative Splicing Database
  Nucleic Acids Res. 32: D64-D69.

• Heike Pospisil, Alexander Herrmann, Ralf H. Bortfeldt, and Jens G. Reich
  EASED: Extended Alternatively Spliced EST Database
  Nucleic Acids Res. 32: D70-D74.

• Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, and Kenta Nakai
  DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
  Nucleic Acids Res. 32: D75-D77.

• Yutaka Suzuki, Riu Yamashita, Sumio Sugano, and Kenta Nakai
  DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
  Nucleic Acids Res. 32: D78-D81.

• Christoph D. Schmid, Viviane Praz, Mauro Delorenzi, Rouaïda Périer, and Philipp Bucher
  The Eukaryotic Promoter Database EPD: the impact of in silico primer extension
  Nucleic Acids Res. 32: D82-D85.

• Twyla T. Pohar, Hao Sun, and Ramana V. Davuluri
  HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development
  Nucleic Acids Res. 32: D86-D90.

• Albin Sandelin, Wynand Alkema, Pär Engström, Wyeth W. Wasserman, and Boris Lenhard
  JASPAR: an open-access database for eukaryotic transcription factor binding profiles
  Nucleic Acids Res. 32: D91-D94.

• Jennifer F. Lee, Jay R. Hesselberth, Lauren Ancel Meyers, and Andrew D. Ellington
  Aptamer Database
  Nucleic Acids Res. 32: D95-D100.

• Jan Wuyts, Guy Perrière, and Yves Van de Peer
  The European ribosomal RNA database
  Nucleic Acids Res. 32: D101-D103.

• Pulcherie Gueneau de Novoa and Kelly P. Williams
  The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts
  Nucleic Acids Res. 32: D104-D108.

• Sam Griffiths-Jones
  The microRNA Registry
  Nucleic Acids Res. 32: D109-D111.

• Cathy H. Wu, Anastasia Nikolskaya, Hongzhan Huang, Lai-Su L. Yeh, Darren A. Natale, C. R. Vinayaka, Zhang-Zhi Hu, Raja Mazumder, Sandeep Kumar, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Leslie Arminski, Yongxing Chen, Jian Zhang, Jorge Louie Cardenas, Sehee Chung, Jorge Castro-Alvear, Georgi Dinkov, and Winona C. Barker
  PIRSF: family classification system at the Protein Information Resource
  Nucleic Acids Res. 32: D112-D114.

• Rolf Apweiler, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria J. Martin, Darren A. Natale, Claire OÕDonovan, Nicole Redaschi, and Lai-Su L. Yeh
  UniProt: the Universal Protein knowledgebase
  Nucleic Acids Res. 32: D115-D119.

• K. Abdulla Bava, M. Michael Gromiha, Hatsuho Uedaira, Koji Kitajima, and Akinori Sarai
  ProTherm, version 4.0: thermodynamic database for proteins and mutants
  Nucleic Acids Res. 32: D120-D121.

• Tao Guo, Sujun Hua, Xinglai Ji, and Zhirong Sun
  DBSubLoc: database of protein subcellular localization
  Nucleic Acids Res. 32: D122-D124.

• S. A. Fernando, P. Selvarani, Soma Das, Ch. Kiran Kumar, Sukanta Mondal, S. Ramakumar, and K. Sekar
  THGS: a web-based database of Transmembrane Helices in Genome Sequences
  Nucleic Acids Res. 32: D125-D128.

• Craig T. Porter, Gail J. Bartlett, and Janet M. Thornton
  The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
  Nucleic Acids Res. 32: D129-D133.

• Nicolas Hulo, Christian J. A. Sigrist, Virginie Le Saux, Petra S. Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, and Amos Bairoch
  Recent improvements to the PROSITE database
  Nucleic Acids Res. 32: D134-D137.

• Alex Bateman, Lachlan Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, and Sean R. Eddy
  The Pfam protein families database
  Nucleic Acids Res. 32: D138-D141.

• Ivica Letunic, Richard R. Copley, Steffen Schmidt, Francesca D. Ciccarelli, Tobias Doerks, Jörg Schultz, Chris P. Ponting, and Peer Bork
  SMART 4.0: towards genomic data integration
  Nucleic Acids Res. 32: D142-D144.

• Thierry Hotelier, Ludovic Renault, Xavier Cousin, Vincent Negre, Pascale Marchot, and Arnaud Chatonnet
  ESTHER, the database of the α/β-hydrolase fold superfamily of proteins
  Nucleic Acids Res. 32: D145-D147.

• David A. Lee, Sandrine Fefeu, Adrian A. Edo-Ukeh, Christine A. Orengo, and Christine Slingsby
  EyeSite: a semi-automated database of protein families in the eye
  Nucleic Acids Res. 32: D148-D152.

• A. Krupa, K. R. Abhinandan, and N. Srinivasan
  KinG: a database of protein kinases in genomes
  Nucleic Acids Res. 32: D153-D155.

• Jean-Christophe Gelly, Jérôme Gracy, Quentin Kaas, Dung Le-Nguyen, Annie Heitz, and Laurent Chiche
  The KNOTTIN website and database: a new information system dedicated to the knottin scaffold
  Nucleic Acids Res. 32: D156-D159.

• Neil D. Rawlings, Dominic P. Tolle, and Alan J. Barrett
  MEROPS: the peptidase database
  Nucleic Acids Res. 32: D160-D164.

• David Ruau, Jorge Duarte, Tarik Ourjdal, Guy Perrière, Vincent Laudet, and Marc Robinson-Rechavi
  Update of NUREBASE: nuclear hormone receptor functional genomics
  Nucleic Acids Res. 32: D165-D167.

• Akihiro Nakao, Maki Yoshihama, and Naoya Kenmochi
  RPG: the Ribosomal Protein Gene database
  Nucleic Acids Res. 32: D168-D170.

• Antoni Hermoso, Daniel Aguilar, Francesc X. Aviles, and Enrique Querol
  TrSDB: a proteome database of transcription factors
  Nucleic Acids Res. 32: D171-D173.

• Michael M. Hoffman, Maksim A. Khrapov, J. Colin Cox, Jianchao Yao, Lingnan Tong, and Andrew D. Ellington
  AANT: the Amino AcidÐNucleotide Interaction Database
  Nucleic Acids Res. 32: D174-D181.

• Makio Tamura, Donna K. Hendrix, Peter S. Klosterman, Nancy R. B. Schimmelman, Steven E. Brenner, and Stephen R. Holbrook
  SCOR: Structural Classification of RNA, version 2.0
  Nucleic Acids Res. 32: D182-D184.

• Jordi Espadaler, Narcis Fernandez-Fuentes, Antonio Hermoso, Enrique Querol, Francesc X. Aviles, Michael J. E. Sternberg, and Baldomero Oliva
  ArchDB: automated protein loop classification as a tool for structural genomics
  Nucleic Acids Res. 32: D185-D188.

• John-Marc Chandonia, Gary Hon, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, and Steven E. Brenner
  The ASTRAL Compendium in 2004
  Nucleic Acids Res. 32: D189-D192.

• R. Aroul Selvam and Rajkumar Sasidharan
  DomIns: a web resource for domain insertions in known protein structures
  Nucleic Acids Res. 32: D193-D195.

• Liam J. McGuffin, Stefano A. Street, Kevin Bryson, S¿ren-Aksel S¿rensen, and David T. Jones
  The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms
  Nucleic Acids Res. 32: D196-D199.

• A. Vinayagam, G. Pugalenthi, R. Rajesh, and R. Sowdhamini
  DSDBASE: a consortium of native and modelled disulphide bonds in proteins
  Nucleic Acids Res. 32: D200-D202.

• Lucy A. Stebbings and Kenji Mizuguchi
  HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database
  Nucleic Acids Res. 32: D203-D207.

• Quentin Kaas, Manuel Ruiz, and Marie-Paule Lefranc
  IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data
  Nucleic Acids Res. 32: D208-D210.

• A. Golovin, T. J. Oldfield, J. G. Tate, S. Velankar, G. J. Barton, H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Hussain, J. M. C. Ionides, M. John, P. A. Keller, E. Krissinel, P. McNeil, A. Naim, R. Newman, A. Pajon, J. Pineda, A. Rachedi, J. Copeland, A. Sitnov, S. Sobhany, A. Suarez-Uruena, G. J. Swaminathan, M. Tagari, S. Tromm, W. Vranken, and K. Henrick
  E-MSD: an integrated data resource for bioinformatics
  Nucleic Acids Res. 32: D211-D216.

• Ursula Pieper, Narayanan Eswar, Hannes Braberg, M. S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Marti-Renom, Andras Fiser, Ben Webb, Daniel Greenblatt, Conrad C. Huang, Thomas E. Ferrin, and Andrej Sali
  MODBASE, a database of annotated comparative protein structure models, and associated resources
  Nucleic Acids Res. 32: D217-D222.

• Philip E. Bourne, Kenneth J. Addess, Wolfgang F. Bluhm, Li Chen, Nita Deshpande, Zukang Feng, Ward Fleri, Rachel Green, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Helge Weissig, John Westbrook, and Helen M. Berman
  The distribution and query systems of the RCSB Protein Data Bank
  Nucleic Acids Res. 32: D223-D225.

• Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, and Alexey G. Murzin
  SCOP database in 2004: refinements integrate structure and sequence family data
  Nucleic Acids Res. 32: D226-D229.

• Jürgen Kopp and Torsten Schwede
  The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models
  Nucleic Acids Res. 32: D230-D234.

• Martin Madera, Christine Vogel, Sarah K. Kummerfeld, Cyrus Chothia, and Julian Gough
  The SUPERFAMILY database in 2004: additions and improvements
  Nucleic Acids Res. 32: D235-D239.

• Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, and Manuela Helmer-Citterich
  SURFACE: a database of protein surface regions for functional annotation
  Nucleic Acids Res. 32: D240-D244.

• Keiran Fleming, Arne Müller, Robert M. MacCallum, and Michael J. E. Sternberg
  3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
  Nucleic Acids Res. 32: D245-D250.

• Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, and David R. Westhead
  TOPS: an enhanced database of protein structural topology
  Nucleic Acids Res. 32: D251-D254.

• Hester M. Wain, Michael J. Lush, Fabrice Ducluzeau, Varsha K. Khodiyar, and Sue Povey
  Genew: the Human Gene Nomenclature Database, 2004 updates
  Nucleic Acids Res. 32: D255-D257.

• Gene Ontology Consortium
  The Gene Ontology (GO) database and informatics resource
  Nucleic Acids Res. 32: D258-D261.

• Evelyn Camon, Michele Magrane, Daniel Barrell, Vivian Lee, Emily Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, and Rolf Apweiler
  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
  Nucleic Acids Res. 32: D262-D266.

• Olivier Bodenreider
  The Unified Medical Language System (UMLS): integrating biomedical terminology
  Nucleic Acids Res. 32: D267-D270.

• Ren Zhang, Hong-Yu Ou, and Chun-Ting Zhang
  DEG: a database of essential genes
  Nucleic Acids Res. 32: D271-D272.

• Karsten Suhre and Jean-Michel Claverie
  FusionDB: a database for in-depth analysis of prokaryotic gene fusion events
  Nucleic Acids Res. 32: D273-D276.

• Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Yasushi Okuno, and Masahiro Hattori
  The KEGG resource for deciphering the genome
  Nucleic Acids Res. 32: D277-D280.

• Naomi Siew, Yaniv Azaria, and Daniel Fischer
  The ORFanage: an ORFan database
  Nucleic Acids Res. 32: D281-D283.

• Qinghu Ren, Katherine H. Kang, and Ian T. Paulsen
  TransportDB: a relational database of cellular membrane transport systems
  Nucleic Acids Res. 32: D284-D288.

• Urmila Kulkarni-Kale, Shriram Bhosle, G. Sunitha Manjari, and A. S. Kolaskar
  VirGen: a comprehensive viral genome resource
  Nucleic Acids Res. 32: D289-D292.

• Shan Sundararaj, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani, Paul Stothard, Michael Ellison, and David S. Wishart
  The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
  Nucleic Acids Res. 32: D293-D295.

• Roy R. Chaudhuri, Arshad M. Khan, and Mark J. Pallen
  coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics
  Nucleic Acids Res. 32: D296-D299.

• Margrethe H. Serres, Sulip Goswami, and Monica Riley
  GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins
  Nucleic Acids Res. 32: D300-D302.

• Heladia Salgado, Socorro Gama-Castro, Agustino Martínez-Antonio, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Martín Peralta-Gil, Delfino Garcia-Alonso, Verónica Jiménez-Jacinto, Alberto Santos-Zavaleta, César Bonavides-Martínez, and Julio Collado-Vides
  RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
  Nucleic Acids Res. 32: D303-D306.

• Aurélien Barré, Antoine de Daruvar, and Alain Blanchard
  MolliGen, a database dedicated to the comparative genomics of Mollicutes
  Nucleic Acids Res. 32: D307-D310.

• Karen R. Christie, Shuai Weng, Rama Balakrishnan, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, and J. Michael Cherry
  Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
  Nucleic Acids Res. 32: D311-D314.

• David Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, and Jean-Luc Souciet for the Génolevures Consortium
  Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts
  Nucleic Acids Res. 32: D315-D318.

• Taro L. Saito, Miwaka Ohtani, Hiroshi Sawai, Fumi Sano, Ayaka Saka, Daisuke Watanabe, Masashi Yukawa, Yoshikazu Ohya, and Shinichi Morishita
  SCMD: Saccharomyces cerevisiae Morphological Database
  Nucleic Acids Res. 32: D319-D322.

• Gaëlle Lelandais, Stéphane Le Crom, Frédéric Devaux, Stéphane Vialette, George M. Church, Claude Jacq, and Philippe Marc
  yMGV: a cross-species expression data mining tool
  Nucleic Acids Res. 32: D323-D325.

• Li Li, Jonathan Crabtree, Steve Fischer, Deborah Pinney, Christian J. Stoeckert, Jr, L. David Sibley, and David S. Roos
  ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
  Nucleic Acids Res. 32: D326-D328.

• Daniela Puiu, Shinichiro Enomoto, Gregory A. Buck, Mitchell S. Abrahamsen, and Jessica C. Kissinger
  CryptoDB: the Cryptosporidium genome resource
  Nucleic Acids Res. 32: D329-D331.

• Lisa Kreppel, Petra Fey, Pascale Gaudet, Eric Just, Warren A. Kibbe, Rex L. Chisholm, and Alan R. Kimmel
  dictyBase: a new Dictyostelium discoideum genome database
  Nucleic Acids Res. 32: D332-D333.

• Junichi Watanabe, Yutaka Suzuki, Masahide Sasaki, and Sumio Sugano
  Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species
  Nucleic Acids Res. 32: D334-D338.

• Christiane Hertz-Fowler, Chris S. Peacock, Valerie Wood, Martin Aslett, Arnaud Kerhornou, Paul Mooney, Adrian Tivey, Matthew Berriman, Neil Hall, Kim Rutherford, Julian Parkhill, Alasdair C. Ivens, Marie-Adele Rajandream, and Bart Barrell
  GeneDB: a resource for prokaryotic and eukaryotic organisms
  Nucleic Acids Res. 32: D339-D343.

• Michael Luchtan, Chetna Warade, D. Brent Weatherly, Wim M. Degrave, Rick L. Tarleton, and Jessica C. Kissinger
  TcruziDB: an integrated Trypanosoma cruzi genome resource
  Nucleic Acids Res. 32: D344-D346.

• Franck Samson, Véronique Brunaud, Sylvain Duchêne, Yannick De Oliveira, Michel Caboche, Alain Lecharny, and Sébastien Aubourg
  FLAGdb⁺⁺: a database for the functional analysis of the Arabidopsis genome
  Nucleic Acids Res. 32: D347-D350.

• S. Mohseni-Zadeh, A. Louis, P. Brézellec, and J.-L. Risler
  PHYTOPROT: a database of clusters of plant proteins
  Nucleic Acids Res. 32: D351-D353.

• Qunfeng Dong, Shannon D. Schlueter, and Volker Brendel
  PlantGDB, plant genome database and analysis tools
  Nucleic Acids Res. 32: D354-D359.

• Shu Ouyang and C. Robin Buell
  The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
  Nucleic Acids Res. 32: D360-D363.

• Manuel Ruiz, Mathieu Rouard, Louis Marie Raboin, Marc Lartaud, Pierre Lagoda, and Brigitte Courtois
  TropGENE-DB, a multi-tropical crop information system
  Nucleic Acids Res. 32: D364-D367.

• Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Lorenz Bülow, and Reinhard Hehl
  AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
  Nucleic Acids Res. 32: D368-D372.

• Heiko Schoof, Rebecca Ernst, Vladimir Nazarov, Lukas Pfeifer, Hans-Werner Mewes, and Klaus F. X. Mayer
  MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics
  Nucleic Acids Res. 32: D373-D376.

• Wenming Zhao, Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, and Jun Wang
  BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
  Nucleic Acids Res. 32: D377-D382.

• Junshi Yazaki, Keiichi Kojima, Kouji Suzuki, Naoki Kishimoto, and Shoshi Kikuchi
  The Rice PIPELINE: a unification tool for plant functional genomics
  Nucleic Acids Res. 32: D383-D387.

• Setsuko Komatsu, Keiichi Kojima, Kouji Suzuki, Kazuo Ozaki, and Kenichi Higo
  Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003
  Nucleic Acids Res. 32: D388-D392.

• Carolyn J. Lawrence, Qunfeng Dong, Mary L. Polacco, Trent E. Seigfried, and Volker Brendel
  MaizeGDB, the community database for maize genetics and genomics
  Nucleic Acids Res. 32: D393-D397.

• Nadim W. Alkharouf and Benjamin F. Matthews
  SGMD: the Soybean Genomics and Microarray Database
  Nucleic Acids Res. 32: D398-D400.

• J. E. Mabey, M. J. Anderson, P. F. Giles, C. J. Miller, T. K. Attwood, N. W. Paton, E. Bornberg-Bauer, G. D. Robson, S. G. Oliver, and D. W. Denning
  CADRE: the Central Aspergillus Data REpository
  Nucleic Acids Res. 32: D401-D405.

• Kristin C. Gunsalus, Wan-Chen Yueh, Philip MacMenamin, and Fabio Piano
  RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects
  Nucleic Acids Res. 32: D406-D410.

• Todd W. Harris, Nansheng Chen, Fiona Cunningham, Marcela Tello-Ruiz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Muller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz, Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth, Paul W. Sternberg, and Lincoln D. Stein
  WormBase: a multi-species resource for nematode biology and genomics
  Nucleic Acids Res. 32: D411-D417.

• Reed J. Kelso, Michael Buszczak, Ana T. Quiñones, Claudia Castiblanco, Stacy Mazzalupo, and Lynn Cooley
  Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster
  Nucleic Acids Res. 32: D418-D420.

• Jagan Srinivasan, Georg W. Otto, Ulrich Kahlow, Robert Geisler, and Ralf J. Sommer
  AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus
  Nucleic Acids Res. 32: D421-D422.

• Todd Wylie, John C. Martin, Michael Dante, Makedonka Dautova Mitreva, Sandra W. Clifton, Asif Chinwalla, Robert H. Waterston, Richard K. Wilson, and James P. McCarter
  Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
  Nucleic Acids Res. 32: D423-D426.

• John Parkinson, Claire Whitton, Ralf Schmid, Marian Thomson, and Mark Blaxter
  NEMBASE: a resource for parasitic nematode ESTs
  Nucleic Acids Res. 32: D427-D430.

• Ida Schomburg, Antje Chang, Christian Ebeling, Marion Gremse, Christian Heldt, Gregor Huhn, and Dietmar Schomburg
  BRENDA, the enzyme database: updates and major new developments
  Nucleic Acids Res. 32: D431-D433.

• Astrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Wolfgang Fleischmann, Sinéad Boyce, Kristian B. Axelsen, Amos Bairoch, Dietmar Schomburg, Keith F. Tipton, and Rolf Apweiler
  IntEnz, the integrated relational enzyme database
  Nucleic Acids Res. 32: D434-D437.

• Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, Alfred Wang, Suzanne Paley, Martha Arnaud, John Pick, Seung Y. Rhee, and Peter D. Karp
  MetaCyc: a multiorganism database of metabolic pathways and enzymes
  Nucleic Acids Res. 32: D438-D442.

• Christian Lemer, Erick Antezana, Fabian Couche, Frédéric Fays, Xavier Santolaria, Rekin's Janky, Yves Deville, Jean Richelle, and Shoshana J. Wodak
  The aMAZE LightBench: a web interface to a relational database of cellular processes
  Nucleic Acids Res. 32: D443-D448.

• Lukasz Salwinski, Christopher S. Miller, Adam J. Smith, Frank K. Pettit, James U. Bowie, and David Eisenberg
  The Database of Interacting Proteins: 2004 update
  Nucleic Acids Res. 32: D449-D451.

• Henning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David Sherman, and Rolf Apweiler
  IntAct: an open source molecular interaction database
  Nucleic Acids Res. 32: D452-D455.

• Ming Chen, Susana Lin, and Ralf Hofestaedt
  STCDB: Signal Transduction Classification Database
  Nucleic Acids Res. 32: D456-D458.

• C. Andreoli, H. Prokisch, K. Hörtnagel, J. C. Mueller, M. Münsterkötter, C. Scharfe, and T. Meitinger
  MitoP2, an integrated database on mitochondrial proteins in yeast and man
  Nucleic Acids Res. 32: D459-D462.

• Dawn Cotter, Purnima Guda, Eoin Fahy, and Shankar Subramaniam
  MitoProteome: mitochondrial protein sequence database and annotation system
  Nucleic Acids Res. 32: D463-D467.

• E. Birney, D. Andrews, P. Bevan, M. Caccamo, G. Cameron, Y. Chen, L. Clarke, G. Coates, T. Cox, J. Cuff, V. Curwen, T. Cutts, T. Down, R. Durbin, E. Eyras, X. M. Fernandez-Suarez, P. Gane, B. Gibbins, J. Gilbert, M. Hammond, H. Hotz, V. Iyer, A. Kahari, K. Jekosch, A. Kasprzyk, D. Keefe, S. Keenan, H. Lehvaslaiho, G. McVicker, C. Melsopp, P. Meidl, E. Mongin, R. Pettett, S. Potter, G. Proctor, M. Rae, S. Searle, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, A. Ureta-Vidal, C. Woodwark, M. Clamp, and T. Hubbard
  Ensembl 2004
  Nucleic Acids Res. 32: D468-D470.

• Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, RIKEN GER Group, GSL Members, Akihiko Konagaya, and Christian Schönbach
  FREP: a database of functional repeats in mouse cDNAs
  Nucleic Acids Res. 32: D471-D475.

• Carol J. Bult, Judith A. Blake, Joel E. Richardson, James A. Kadin, Janan T. Eppig, and the Mouse Genome Database Group
  The Mouse Genome Database (MGD): integrating biology with the genome
  Nucleic Acids Res. 32: D476-D481.

• Petr Divina and Jirí Forejt
  The Mouse SAGE Site: database of public mouse SAGE libraries
  Nucleic Acids Res. 32: D482-D483.

• Hirohide Uenishi, Tomoko Eguchi, Kohei Suzuki, Tetsuya Sawazaki, Daisuke Toki, Hiroki Shinkai, Naohiko Okumura, Noriyuki Hamasima, and Takashi Awata
  PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries
  Nucleic Acids Res. 32: D484-D488.

• Tal Dagan, Rotem Sorek, Eilon Sharon, Gil Ast, and Dan Graur
  AluGene: a database of Alu elements incorporated within protein-coding genes
  Nucleic Acids Res. 32: D489-D492.

• Donna Karolchik, Angela S. Hinrichs, Terrence S. Furey, Krishna M. Roskin, Charles W. Sugnet, David Haussler, and W. James Kent
  The UCSC Table Browser data retrieval tool
  Nucleic Acids Res. 32: D493-D496.

• Suraj Peri, J. Daniel Navarro, Troels Z. Kristiansen, Ramars Amanchy, Vineeth Surendranath, Babylakshmi Muthusamy, T. K. B. Gandhi, K. N. Chandrika, Nandan Deshpande, Shubha Suresh, B. P. Rashmi, K. Shanker, N. Padma, Vidya Niranjan, H. C. Harsha, Naveen Talreja, B. M. Vrushabendra, M. A. Ramya, A. J. Yatish, Mary Joy, H. N. Shivashankar, M. P. Kavitha, Minal Menezes, Dipanwita Roy Choudhury, Neelanjana Ghosh, R. Saravana, Sreenath Chandran, Sujatha Mohan, Chandra Kiran Jonnalagadda, C. K. Prasad, Chandan Kumar-Sinha, Krishna S. Deshpande, and Akhilesh Pandey
  Human protein reference database as a discovery resource for proteomics
  Nucleic Acids Res. 32: D497-D501.

• Reiko Kikuno, Takahiro Nagase, Manabu Nakayama, Hisashi Koga, Noriko Okazaki, Daisuke Nakajima, and Osamu Ohara
  HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE
  Nucleic Acids Res. 32: D502-D504.

• Detlev Bannasch, Alexander Mehrle, Karl-Heinz Glatting, Rainer Pepperkok, Annemarie Poustka, and Stefan Wiemann
  LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system
  Nucleic Acids Res. 32: D505-D508.

• Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, and C. Victor Jongeneel
  trome, trEST and trGEN: databases of predicted protein sequences
  Nucleic Acids Res. 32: D509-D511.

• Paul N. Schofield, Jonathan B. L. Bard, Catherine Booth, Jacques Boniver, Vincenzo Covelli, Philippe Delvenne, Michele Ellender, Wilhelm Engstrom, Wolfgang Goessner, Michael Gruenberger, Heinz Hoefler, John Hopewell, Mariatheresa Mancuso, Carmel Mothersill, Christopher S. Potten, Leticia Quintanilla-Fend, Bjorn Rozell, Hannu Sariola, John P. Sundberg, and Andrew Ward
  Pathbase: a database of mutant mouse pathology
  Nucleic Acids Res. 32: D512-D515.

• D. Fredman, G. Munns, D. Rios, F. Sjöholm, M. Siegfried, B. Lenhard, H. Lehväslaiho, and A. J. Brookes
  HGVbase: a curated resource describing human DNA variation and phenotype relationships
  Nucleic Acids Res. 32: D516-D519.

• Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Simon Kasif, and Jie Liang
  topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
  Nucleic Acids Res. 32: D520-D522.

• Keiko Akagi, Takeshi Suzuki, Robert M. Stephens, Nancy A. Jenkins, and Neal G. Copeland
  RTCGD: retroviral tagged cancer gene database
  Nucleic Acids Res. 32: D523-D527.

• Bernice R. Packer, Meredith Yeager, Brian Staats, Robert Welch, Andrew Crenshaw, Maureen Kiley, Andrew Eckert, Michael Beerman, Edward Miller, Andrew Bergen, Nathaniel Rothman, Robert Strausberg, and Stephen J. Chanock
  SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes
  Nucleic Acids Res. 32: D528-D532.

• Suisheng Tang, Hao Han, and Vladimir B. Bajic
  ERGDB: Estrogen Responsive Genes Database
  Nucleic Acids Res. 32: D533-D536.

• George P. Patrinos, Belinda Giardine, Cathy Riemer, Webb Miller, David H. K. Chui, Nicholas P. Anagnou, Henri Wajcman, and Ross C. Hardison
  Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies
  Nucleic Acids Res. 32: D537-D541.

• Viviane Praz, Vidhya Jagannathan, and Philipp Bucher
  CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature
  Nucleic Acids Res. 32: D542-D547.

• Itoshi Nikaido, Chika Saito, Akiko Wakamoto, Yasuhiro Tomaru, Takahiro Arakawa, Yoshihide Hayashizaki, and Yasushi Okazaki
  EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes
  Nucleic Acids Res. 32: D548-D551.

• Axel Visel, Christina Thaller, and Gregor Eichele
  GenePaint.org: an atlas of gene expression patterns in the mouse embryo
  Nucleic Acids Res. 32: D552-D556.

• Christine To, Trevor Epp, Tammy Reid, Qing Lan, Mei Yu, Carol Y. J. Li, Minako Ohishi, Paula Hant, Nora Tsao, Guillermo Casallo, Janet Rossant, Lucy R. Osborne, and William L. Stanford
  The Centre for Modeling Human Disease Gene Trap resource
  Nucleic Acids Res. 32: D557-D559.

• C. Wiederkehr, R. Basavaraj, C. Sarrauste de Menthière, L. Hermida, R. Koch, U. Schlecht, A. Amon, S. Brachat, M. Breitenbach, P. Briza, S. Caburet, M. Cherry, R. Davis, A. Deutschbauer, H. G. Dickinson, T. Dumitrescu, M. Fellous, A. Goldman, J. A. Grootegoed, R. Hawley, R. Ishii, B. Jégou, R. J. Kaufman, F. Klein, N. Lamb, B. Maro, K. Nasmyth, A. Nicolas, T. Orr-Weaver, P. Philippsen, C. Pineau, K. P. Rabitsch, V. Reinke, H. Roest, W. Saunders, M. Schröder, T. Schedl, M. Siep, A. Villeneuve, D. J. Wolgemuth, M. Yamamoto, D. Zickler, R. E. Esposito, and M. Primig
  GermOnline, a cross-species community knowledgebase on germ cell differentiation
  Nucleic Acids Res. 32: D560-D567.

• David P. Hill, Dale A. Begley, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Constance M. Smith, Jon S. Beal, Lori E. Corbani, Judith A. Blake, Janan T. Eppig, James A. Kadin, Joel E. Richardson, and Martin Ringwald
  The mouse Gene Expression Database (GXD): updates and enhancements
  Nucleic Acids Res. 32: D568-D571.

• Sung-Ho Goh, Y. Terry Lee, Gerard G. Bouffard, and Jeffery L. Miller
  Hembase: browser and genome portal for hematology and erythroid biology
  Nucleic Acids Res. 32: D572-D574.

• David J. Craigon, Nick James, John Okyere, Janet Higgins, Joan Jotham, and Sean May
  NASCArrays: a repository for microarray data generated by NASCÕs transcriptomics service
  Nucleic Acids Res. 32: D575-D577.

• Josephine Chen, Po Zhao, Donald Massaro, Linda B. Clerch, Richard R. Almon, Debra C. DuBois, William J. Jusko, and Eric P. Hoffman
  The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface
  Nucleic Acids Res. 32: D578-D581.

• György Babnigg and Carol S. Giometti
  GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes
  Nucleic Acids Res. 32: D582-D585.

• M. Brahmachary, S. P. T. Krishnan, J. L. Y. Koh, A. M. Khan, S. H. Seah, T. W. Tan, V. Brusic, and V. B. Bajic
  ANTIMIC: a database of antimicrobial sequences
  Nucleic Acids Res. 32: D586-D589.

• Zhe Wang and Guangshun Wang
  APD: the Antimicrobial Peptide Database
  Nucleic Acids Res. 32: D590-D592.

• Lee Whitmore and B. A. Wallace
  The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols
  Nucleic Acids Res. 32: D593-D594.

• Feng Liang, Udayakumar Matrubutham, Babak Parvizi, Jessica Yen, Daniel Duan, Jyotika Mirchandani, Sandra Hashima, Uyen Nguyen, Eric Ubil, Jake Loewenheim, Xin Yu, Sara Sipes, Wendy Williams, Ling Wang, Robert Bennett, and John Carrino
  ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection
  Nucleic Acids Res. 32: D595-D599.

Latest update: January 14, 2004

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