Nucleic Acids Research, Volume 33

Volume 33, Database-Issue, January 1 2005

• Alex Bateman:
  Editorial. 1
  Electronic Edition (link) BibTeX
• Dov Greenbaum, Andrew Smith, Mark Gerstein:
  Editorial. 3-4
  Electronic Edition (link) BibTeX

• Michael Y. Galperin:
  The Molecular Biology Database Collection: 2005 update. 5-24
  Electronic Edition (link) BibTeX
• Yoshio Tateno, Naruya Saitou, Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori:
  DDBJ in collaboration with mass-sequencing teams on annotation. 25-28
  Electronic Edition (link) BibTeX
• Carola Kanz, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Alastair Baldwin, Kirsty Bates, Paul Browne, Alexandra van den Broek, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Federico Garcia Diez, Nicola Harte, Tamara Kulikova, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Siamak Sobhany, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler:
  The EMBL Nucleotide Sequence Database. 29-33
  Electronic Edition (link) BibTeX
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
  GenBank. 34-38
  Electronic Edition (link) BibTeX
• David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Wolfgang Helmberg, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Joan U. Pontius, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Grigory Starchenko, Tugba O. Suzek, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko:
  Database resources of the National Center for Biotechnology Information. 39-45
  Electronic Edition (link) BibTeX
• Catherine Brooksbank, Graham Cameron, Janet M. Thornton:
  The European Bioinformatics Institute's data resources: towards systems biology. 46-53
  Electronic Edition (link) BibTeX
• Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova:
  Entrez Gene: gene-centered information at NCBI. 54-58
  Electronic Edition (link) BibTeX
• Adel Khelifi, Laurent Duret, Dominique Mouchiroud:
  HOPPSIGEN: a database of human and mouse processed pseudogenes. 59-66
  Electronic Edition (link) BibTeX
• Victor G. Levitsky, Aleksey V. Katokhin, Olga A. Podkolodnaya, Dagmara P. Furman, Nikolay A. Kolchanov:
  NPRD: Nucleosome Positioning Region Database. 67-70
  Electronic Edition (link) BibTeX
• Yuandan Lee, Jennifer Tsai, S. Sunkara, Svetlana Karamycheva, Geo Pertea, Razvan Sultana, Valentin Antonescu, Agnes P. Chan, Foo Cheung, John Quackenbush:
  The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. 71-74
  Electronic Edition (link) BibTeX
• Pora Kim, Namshin Kim, Younghee Lee, Bumjin Kim, Youngah Shin, Sanghyuk Lee:
  ECgene: genome annotation for alternative splicing. 75-79
  Electronic Edition (link) BibTeX
• Hsien-Da Huang, Jorng-Tzong Horng, Feng-Mao Lin, Yu-Chung Chang, Chen-Chia Huang:
  SpliceInfo: an information repository for mRNA alternative splicing in human genome. 80-85
  Electronic Edition (link) BibTeX
• Endre Barta, Endre Sebestyén, Tamás B. Pálfy, Gábor Tóth, Csaba P. Ortutay, László Patthy:
  DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. 86-90
  Electronic Edition (link) BibTeX
• Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva:
  The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. 91-97
  Electronic Edition (link) BibTeX
• Abel D. González, Vladimir Espinosa, Ana Tereza R. Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides:
  TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. 98-102
  Electronic Edition (link) BibTeX
• Fang Zhao, Zhenyu Xuan, Lihua Liu, Michael Q. Zhang:
  TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. 103-107
  Electronic Edition (link) BibTeX
• Matthias Truss, Maciej Swat, Szymon M. Kielbasa, Reinhold Schäfer, Hanspeter Herzel, Christian Hagemeier:
  HuSiDa - the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. 108-111
  Electronic Edition (link) BibTeX
• Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, Runsheng Chen:
  NONCODE: an integrated knowledge database of non-coding RNAs. 112-115
  Electronic Edition (link) BibTeX
• Haibo Zhang, Jun Hu, Michael Recce, Bin Tian:
  PolyA_DB: a database for mammalian mRNA polyadenylation. 116-120
  Electronic Edition (link) BibTeX
• Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, Alex Bateman:
  Rfam: annotating non-coding RNAs in complete genomes. 121-124
  Electronic Edition (link) BibTeX
• Ken C. Pang, Stuart Stephen, Pär G. Engström, Khairina Tajul-Arifin, Weisan Chen, Claes Wahlestedt, Boris Lenhard, Yoshihide Hayashizaki, John S. Mattick:
  RNAdb - a comprehensive mammalian noncoding RNA database. 125-130
  Electronic Edition (link) BibTeX
• Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer:
  siRNAdb: a database of siRNA sequences. 131-134
  Electronic Edition (link) BibTeX
• James A. McCloskey, Jef Rozenski:
  The Small Subunit rRNA Modification Database. 135-138
  Electronic Edition (link) BibTeX
• Mathias Sprinzl, Konstantin S. Vassilenko:
  Compilation of tRNA sequences and sequences of tRNA genes. 139-140
  Electronic Edition (link) BibTeX
• Flavio Mignone, Giorgio Grillo, Flavio Licciulli, Michele Iacono, Sabino Liuni, Paul Kersey, Jorge Duarte, Cecilia Saccone, Graziano Pesole:
  UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. 141-146
  Electronic Edition (link) BibTeX
• Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, Nicholas Lamb:
  PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. 147-153
  Electronic Edition (link) BibTeX
• Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, María J. Martín, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L. Yeh:
  The Universal Protein Resource (UniProt). 154-159
  Electronic Edition (link) BibTeX
• Sven Mika, Burkhard Rost:
  NMPdb: Database of Nuclear Matrix Proteins. 160-163
  Electronic Edition (link) BibTeX
• Sébastien Rey, Michael Acab, Jennifer L. Gardy, Matthew R. Laird, Katalin de Fays, Christophe G. Lambert, Fiona S. L. Brinkman:
  PSORTdb: a protein subcellular localization database for bacteria. 164-168
  Electronic Edition (link) BibTeX
• Yunjia Chen, Yong Zhang, Yanbin Yin, Ge Gao, Songgang Li, Ying Jiang, Xiaocheng Gu, Jingchu Luo:
  SPD - a web-based secreted protein database. 169-173
  Electronic Edition (link) BibTeX
• Ya-Hui Chang, Wen-Hui Su, Tso-Ching Lee, Hsiao-Fang Sunny Sun, Chia-Hsiang Chen, Wen-Harn Pan, Shih-Feng Tsai, Yuh-Shan Jou:
  TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations. 174-177
  Electronic Edition (link) BibTeX
• Qiaojuan Jane Su, Lin Lu, Serge Saxonov, Douglas L. Brutlag:
  eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. 178-182
  Electronic Edition (link) BibTeX
• Vladimir A. Ivanisenko, Sergey S. Pintus, Dmitry A. Grigorovich, Nikolay A. Kolchanov:
  PDBSite: a database of the 3D structure of protein functional sites. 183-187
  Electronic Edition (link) BibTeX
• Andreas Heger, Christopher Andrew Wilton, Ashwin Sivakumar, Liisa Holm:
  ADDA: a domain database with global coverage of the protein universe. 188-191
  Electronic Edition (link) BibTeX
• Aron Marchler-Bauer, John B. Anderson, Praveen F. Cherukuri, Carol DeWeese-Scott, Lewis Y. Geer, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, Stephen H. Bryant:
  CDD: a Conserved Domain Database for protein classification. 192-196
  Electronic Edition (link) BibTeX
• Saraswathi Abhiman, Erik L. L. Sonnhammer:
  FunShift: a database of function shift analysis on protein subfamilies. 197-200
  Electronic Edition (link) BibTeX
• Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu:
  InterPro, progress and status in 2005. 201-205
  Electronic Edition (link) BibTeX
• Shu-Hsien Sheu, David R. Lancia Jr., Karl H. Clodfelter, Melissa R. Landon, Sandor Vajda:
  PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. 206-211
  Electronic Edition (link) BibTeX
• Catherine Bru, Emmanuel Courcelle, Sébastien Carrère, Yoann Beausse, Sandrine Dalmar, Daniel Kahn:
  The ProDom database of protein domain families: more emphasis on 3D. 212-215
  Electronic Edition (link) BibTeX
• Noam Kaplan, Ori Sasson, Uri Inbar, Moriah Friedlich, Menachem Fromer, Hillel Fleischer, Elon Portugaly, Nathan Linial, Michal Linial:
  ProtoNet 4.0: A hierarchical classification of one million protein sequences. 216-218
  Electronic Edition (link) BibTeX
• James A. Casbon, Mansoor A. S. Saqi:
  S4: structure-based sequence alignments of SCOP superfamilies. 219-222
  Electronic Edition (link) BibTeX
• Kristian Vlahovicek, László Kaján, Vilmos Ágoston, Sándor Pongor:
  The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. 223-225
  Electronic Edition (link) BibTeX
• Thomas Meinel, Antje Krause, Hannes Luz, Martin Vingron, Eike Staub:
  The SYSTERS Protein Family Database in 2005. 226-229
  Electronic Edition (link) BibTeX
• Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
  REBASE - restriction enzymes and DNA methyltransferases. 230-232
  Electronic Edition (link) BibTeX
• Nita Deshpande, Kenneth J. Addess, Wolfgang Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John D. Westbrook, Helen M. Berman, Philip E. Bourne:
  The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. 233-237
  Electronic Edition (link) BibTeX
• Jae-Min Shin, Doo-Ho Cho:
  PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. 238-241
  Electronic Edition (link) BibTeX
• Thomas Lütteke, Martin Frank, Claus-Wilhelm von der Lieth:
  Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. 242-246
  Electronic Edition (link) BibTeX
• Frances M. G. Pearl, Annabel E. Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony E. Lewis, Christopher Bennett, Russell L. Marsden, Alastair Grant, David Lee, Adrian Akpor, Michael Maibaum, Andrew P. Harrison, Timothy Dallman, Gabrielle A. Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline Johnston, Antonio Sillero, Janet M. Thornton, Christine A. Orengo:
  The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. 247-251
  Electronic Edition (link) BibTeX
• Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
  GenDiS: Genomic Distribution of protein structural domain Superfamilies. 252-255
  Electronic Edition (link) BibTeX
• Véronique Giudicelli, Denys Chaume, Marie-Paule Lefranc:
  IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. 256-261
  Electronic Edition (link) BibTeX
• Samir S. Velankar, P. McNeil, V. Mittard-Runte, A. Suarez, Daniel Barrell, Rolf Apweiler, Kim Henrick:
  E-MSD: an integrated data resource for bioinformatics. 262-265
  Electronic Edition (link) BibTeX
• Roman A. Laskowski, Victor V. Chistyakov, Janet M. Thornton:
  PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. 266-268
  Electronic Edition (link) BibTeX
• Goran Neshich, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Ivan P. Pinto, Juliana F. Palandrani, João N. Krauchenco, Christian Baudet, Arnaldo J. Montagner, Roberto H. Higa:
  STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. 269-274
  Electronic Edition (link) BibTeX
• Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon:
  PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. 275-278
  Electronic Edition (link) BibTeX
• Kate F. Fulton, Glyn L. Devlin, Rachel A. Jodun, Linda Silvestri, Stephen P. Bottomley, Alan R. Fersht, Ashley M. Buckle:
  PFD: a database for the investigation of protein folding kinetics and stability. 279-283
  Electronic Edition (link) BibTeX
• Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody A. Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano, Paul D. Thomas:
  The PANTHER database of protein families, subfamilies, functions and pathways. 284-288
  Electronic Edition (link) BibTeX
• Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, Russ B. Altman:
  Biomedical term mapping databases. 289-293
  Electronic Edition (link) BibTeX
• James R. Cole, B. Chai, Ryan J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, George M. Garrity, James M. Tiedje:
  The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. 294-296
  Electronic Edition (link) BibTeX
• Paul Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, Alexander Kanapin, Ujjwal Das, Karine Michoud, Isabelle Phan, Alexandre Gattiker, Tamara Kulikova, Nadeem Faruque, Karyn Duggan, Peter Mclaren, Britt Reimholz, Laurent Duret, Simon Penel, Ingmar Reuter, Rolf Apweiler:
  Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. 297-302
  Electronic Edition (link) BibTeX
• José M. Peregrin-Alvarez, Andrew Yam, Gaya Sivakumar, John Parkinson:
  PartiGeneDB - collating partial genomes. 303-307
  Electronic Edition (link) BibTeX
• M. Louise Riley, Thorsten Schmidt, Christian Wagner, Hans-Werner Mewes, Dmitrij Frishman:
  The PEDANT genome database in 2005. 308-310
  Electronic Edition (link) BibTeX
• Elliot J. Lefkowitz, Chris Upton, Shankar S. Changayil, Charles Buck, Paula Traktman, R. Mark L. Buller:
  Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. 311-316
  Electronic Edition (link) BibTeX
• Paul Stothard, Gary H. Van Domselaar, Savita Shrivastava, Anchi Guo, Brian O'Neill, Joseph A. Cruz, Michael Ellison, David S. Wishart:
  BacMap: an interactive picture atlas of annotated bacterial genomes. 317-320
  Electronic Edition (link) BibTeX
• Hiroyuki Ogata, Jean-Michel Claverie:
  Metagrowth: a new resource for the building of metabolic hypotheses in microbiology. 321-324
  Electronic Edition (link) BibTeX
• Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, Qi Jin:
  VFDB: a reference database for bacterial virulence factors. 325-328
  Electronic Edition (link) BibTeX
• Raju V. Misra, Richard S. P. Horler, Wolfgang Reindl, Igor Goryanin, Gavin H. Thomas:
  EchoBASE: an integrated post-genomic database for Escherichia coli. 329-333
  Electronic Edition (link) BibTeX
• Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp:
  EcoCyc: a comprehensive database resource for Escherichia coli. 334-337
  Electronic Edition (link) BibTeX
• Geoffrey L. Winsor, Raymond Lo, Shannan J. Ho Sui, Korine S. E. Ung, Shao-Shan Huang, Dean Cheng, Wai-Kay Ho Ching, Robert E. W. Hancock, Fiona S. L. Brinkman:
  Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. 338-343
  Electronic Edition (link) BibTeX
• Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy, K. R. Rajyashri, Villoo Morawala Patell, Chris Bowler:
  The Diatom EST Database. 344-347
  Electronic Edition (link) BibTeX
• Leandro Hermida, Sophie Brachat, Sylvia Voegeli, Peter Philippsen, Michael Primig:
  The Ashbya Genome Database (AGD) - a tool for the yeast community and genome biologists. 348-352
  Electronic Edition (link) BibTeX
• C. d'Enfert, S. Goyard, S. Rodriguez-Arnaveilhe, L. Frangeul, L. Jones, Fredj Tekaia, O. Bader, Antje Albrecht, L. Castillo, A. Dominguez, J. F. Ernst, C. Fradin, C. Gaillardin, S. Garcia-Sanchez, P. de Groot, B. Hube, F. M. Klis, S. Krishnamurthy, D. Kunze, M.-C. Lopez, A. Mavor, N. Martin, I. Moszer, D. Onésime, J. Perez Martin, R. Sentandreu, E. Valentin, A. J. P. Brown:
  CandidaDB: a genome database for Candida albicans pathogenomics. 353-357
  Electronic Edition (link) BibTeX
• Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Gail Binkley, Christopher Lane, Stuart R. Miyasato, Gavin Sherlock:
  The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. 358-363
  Electronic Edition (link) BibTeX
• Ulrich Güldener, Martin Münsterkötter, Gabi Kastenmüller, Normann Strack, Jacques van Helden, Christian Lemer, J. Richelles, Shoshana J. Wodak, J. García-Martínez, J. E. Pérez-Ortín, Holger Michael, Andreas Kaps, E. Talla, Bernard Dujon, B. André, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, Hans-Werner Mewes:
  CYGD: the Comprehensive Yeast Genome Database. 364-368
  Electronic Edition (link) BibTeX
• Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Ilona Pylvänäinen, Graham J. L. Kemp, Olle Nerman, Anders Blomberg:
  PROPHECY - a database for high-resolution phenomics. 369-373
  Electronic Edition (link) BibTeX
• Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Anand Sethuraman, Shuai Weng, David Botstein, J. Michael Cherry:
  Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). 374-377
  Electronic Edition (link) BibTeX
• Michael Riffle, Lars Malmström, Trisha N. Davis:
  The Yeast Resource Center Public Data Repository. 378-382
  Electronic Edition (link) BibTeX
• Nansheng Chen, Todd W. Harris, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Payan Canaran, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Fiona Cunningham, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, Shraddha Pai, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz, Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth, Paul W. Sternberg, Lincoln D. Stein:
  WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. 383-389
  Electronic Edition (link) BibTeX
• Rachel A. Drysdale, Madeline A. Crosby:
  FlyBase: genes and gene models. 390-395
  Electronic Edition (link) BibTeX
• Andre R. O. Cavalcanti, Thomas H. Clarke, Laura F. Landweber:
  MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates. 396-398
  Electronic Edition (link) BibTeX
• Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, Guo Yu, Haifeng Yuan, Yafeng Hu, Ruiqiang Li, Tao Feng, Chen Ye, Cheng Lu, Jun Wang, Songgang Li, Gane Ka-Shu Wong, Huanming Yang, Jian Wang, Zhonghuai Xiang, Zeyang Zhou, Jun Yu:
  SilkDB: a knowledgebase for silkworm biology and genomics. 399-402
  Electronic Edition (link) BibTeX
• M. D. Prasad, M. Muthulakshmi, K. P. Arunkumar, M. Madhu, Vattipally B. Sreenu, V. Pavithra, Buddhaditta Bose, Hampapathalu A. Nagarajaram, K. Mita, T. Shimada, Javaregowda Nagaraju:
  SilkSatDb: a microsatellite database of the silkworm, Bombyx mori. 403-406
  Electronic Edition (link) BibTeX
• Nozomi Nagano:
  EzCatDB: the Enzyme Catalytic-mechanism Database. 407-412
  Electronic Edition (link) BibTeX
• Amelie Stein, Robert B. Russell, Patrick Aloy:
  3did: interacting protein domains of known three-dimensional structure. 413-417
  Electronic Edition (link) BibTeX
• C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, M. Bajec, K. Bantoft, Doron Betel, B. Bobechko, K. Boutilier, E. Burgess, K. Buzadzija, R. Cavero, C. D'Abreo, Ian Donaldson, D. Dorairajoo, M. J. Dumontier, M. R. Dumontier, V. Earles, R. Farrall, Howard J. Feldman, E. Garderman, Y. Gong, R. Gonzaga, V. Grytsan, E. Gryz, V. Gu, E. Haldorsen, A. Halupa, R. Haw, A. Hrvojic, L. Hurrell, Ruth Isserlin, F. Jack, F. Juma, A. Khan, T. Kon, S. Konopinsky, V. Le, E. Lee, S. Ling, M. Magidin, J. Moniakis, J. Montojo, S. Moore, B. Muskat, I. Ng, J. P. Paraiso, B. Parker, Greg Pintilie, R. Pirone, John J. Salama, S. Sgro, T. Shan, Y. Shu, J. Siew, D. Skinner, Kevin A. Snyder, R. Stasiuk, D. Strumpf, Brigitte Tuekam, S. Tao, Z. Wang, M. White, R. Willis, Cheryl Wolting, S. Wong, A. Wrong, C. Xin, R. Yao, B. Yates, S. Zhang, K. Zheng, Tony Pawson, B. F. Francis Ouellette, Christopher W. V. Hogue:
  The Biomolecular Interaction Network Database and related tools 2005 update. 418-424
  Electronic Edition (link) BibTeX
• Elena A. Ananko, Nikolay L. Podkolodny, Irina L. Stepanenko, Olga A. Podkolodnaya, D. A. Rasskazov, D. S. Miginsky, Vitali A. Likhoshvai, Alexander V. Ratushny, N. N. Podkolodnaya, Nikolay A. Kolchanov:
  GeneNet in 2005. 425-427
  Electronic Edition (link) BibTeX
• G. Joshi-Tope, Marc Gillespie, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Bernard de Bono, Bijay Jassal, G. R. Gopinath, G. R. Wu, Lisa Matthews, Suzanna Lewis, Ewan Birney, Lincoln Stein:
  Reactome: a knowledgebase of biological pathways. 428-432
  Electronic Edition (link) BibTeX
• Christian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork:
  STRING: known and predicted protein-protein associations, integrated and transferred across organisms. 433-437
  Electronic Edition (link) BibTeX
• Jing Wang, Ximiao He, Jue Ruan, Mingtao Dai, Jie Chen, Yong Zhang, Yafeng Hu, Chen Ye, Shengting Li, Lijuan Cong, Lin Fang, Bin Liu, Songgang Li, Jian Wang, David W. Burt, Gane Ka-Shu Wong, Jun Yu, Huanming Yang, Jun Wang:
  ChickVD: a sequence variation database for the chicken genome. 438-441
  Electronic Edition (link) BibTeX
• Vamsi Veeramachaneni, Wojciech Makalowski:
  DED: Database of Evolutionary Distances. 442-446
  Electronic Edition (link) BibTeX
• Tim J. P. Hubbard, D. Andrews, Mario Cáccamo, Graham Cameron, Yuan Chen, Michele E. Clamp, Laura Clarke, G. Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas Down, Richard Durbin, X. M. Fernandez-Suarez, James Gilbert, Martin Hammond, J. Herrero, H. Hotz, Kevin L. Howe, V. Iyer, K. Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, S. Keenan, Felix Kokocinski, D. London, I. Longden, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Simon C. Potter, Glenn Proctor, Mark Rae, D. Rios, M. Schuster, Stephen M. J. Searle, J. Severin, Guy Slater, Damian Smedley, James Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, S. Trevanion, Abel Ureta-Vidal, J. Vogel, S. White, Cara Woodwark, Ewan Birney:
  Ensembl 2005. 447-453
  Electronic Edition (link) BibTeX
• Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, W. James Kent:
  The UCSC Proteome Browser. 454-458
  Electronic Edition (link) BibTeX
• J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, Patrick Meidl, Stephen M. J. Searle, Jim Stalker, R. Storey, S. Trevanion, L. G. Wilming, Tim J. P. Hubbard:
  The Vertebrate Genome Annotation (Vega) database. 459-465
  Electronic Edition (link) BibTeX
• Laura Elnitski, Belinda Giardine, Prachi Shah, Yi Zhang, Cathy Riemer, Matthew Weirauch, Richard Burhans, Webb Miller, Ross C. Hardison:
  Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. 466-470
  Electronic Edition (link) BibTeX
• Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake:
  The Mouse Genome Database (MGD): from genes to mice - a community resource for mouse biology. 471-475
  Electronic Edition (link) BibTeX
• Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer:
  Inparanoid: a comprehensive database of eukaryotic orthologs. 476-480
  Electronic Edition (link) BibTeX
• Eric Bazin, Laurent Duret, Simon Penel, Nicolas Galtier:
  Polymorphix: a sequence polymorphism database. 481-484
  Electronic Edition (link) BibTeX
• Norberto de la Cruz, Susan Bromberg, Dean Pasko, Mary Shimoyama, Simon N. Twigger, Jiali Chen, Chin-Fu Chen, Chunyu Fan, Cindy Foote, Gopal R. Gopinath, Glenn Harris, Aubrey Hughes, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Natalya Nenasheva, Jeff Nie, Rajni Nigam, Victoria Petri, Dorothy Reilly, Weiye Wang, Wenhua Wu, Angela Zuniga-Meyer, Lan Zhao, Anne E. Kwitek, Peter J. Tonellato, Howard J. Jacob:
  The Rat Genome Database (RGD): developments towards a phenome database. 485-491
  Electronic Edition (link) BibTeX
• Greta Petersen, Per Johnson, Lars Andersson, Karin Klinga-Levan, Pedro M. Gómez-Fabre, Fredrik Ståhl:
  RatMap - rat genome tools and data. 492-494
  Electronic Edition (link) BibTeX
• Christian Roth, Matthew J. Betts, Pär Steffansson, Gisle Sælensminde, David A. Liberles:
  The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. 495-497
  Electronic Edition (link) BibTeX
• Tobias Penzkofer, Thomas Dandekar, Tomasz Zemojtel:
  L1Base: from functional annotation to prediction of active LINE-1 elements. 498-500
  Electronic Edition (link) BibTeX
• Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott:
  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. 501-504
  Electronic Edition (link) BibTeX
• Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, Sandro Banfi:
  DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. 505-510
  Electronic Edition (link) BibTeX
• Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia:
  HCAD, closing the gap between breakpoints and genes. 511-513
  Electronic Edition (link) BibTeX
• Ada Hamosh, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, Victor A. McKusick:
  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. 514-517
  Electronic Edition (link) BibTeX
• Hyo Jin Kang, Kyoung Oak Choi, Byung-Dong Kim, Sangsoo Kim, Young Joo Kim:
  FESD: a Functional Element SNPs Database in human. 518-522
  Electronic Edition (link) BibTeX
• James Robinson, Matthew J. Waller, Peter Stoehr, Steven G. E. Marsh:
  IPD - the Immuno Polymorphism Database. 523-526
  Electronic Edition (link) BibTeX
• Joke Reumers, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Francois Stricher, Luis Serrano, Frederic Rousseau:
  SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. 527-532
  Electronic Edition (link) BibTeX
• Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai:
  Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. 533-536
  Electronic Edition (link) BibTeX
• João Pedro de Magalhães, Joana Costa, Olivier Toussaint:
  HAGR: the Human Ageing Genomic Resources. 537-543
  Electronic Edition (link) BibTeX
• Luc J. Smink, Erin M. Helton, Barry C. Healy, Christopher C. Cavnor, Alex C. Lam, Daisy Flamez, Oliver S. Burren, Yang Wang, Geoffrey E. Dolman, David B. Burdick, Vincent H. Everett, Gustavo Glusman, Davide Laneri, Lee Rowen, Helen Schuilenburg, Neil M. Walker, Josyf Mychaleckyj, Linda S. Wicker, Decio L. Eizirik, John A. Todd, Nathan Goodman:
  T1DBase, a community web-based resource for type 1 diabetes research. 544-549
  Electronic Edition (link) BibTeX
• Yasuhiro Kasai, Shin-ichi Hashimoto, Tomoyuki Yamada, Jun Sese, Sumio Sugano, Kouji Matsushima, Shinichi Morishita:
  5'SAGE: 5'-end Serial Analysis of Gene Expression database. 550-552
  Electronic Edition (link) BibTeX
• Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Niran Abeygunawardena, Sergio Contrino, R. Coulson, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Misha Kapushesky, P. Lilja, Gaurab Mukherjee, Ahmet Oezcimen, Tim Rayner, Philippe Rocca-Serra, Anjan Sharma, Susanna-Assunta Sansone, Alvis Brazma:
  ArrayExpress - a public repository for microarray gene expression data at the EBI. 553-555
  Electronic Edition (link) BibTeX
• Maxim Shklar, Liora Strichman-Almashanu, Orit Shmueli, Michael Shmoish, Marilyn Safran, Doron Lancet:
  GeneTide - Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases. 556-561
  Electronic Edition (link) BibTeX
• Tanya Barrett, Tugba O. Suzek, Dennis B. Troup, Stephen E. Wilhite, Wing-Chi Ngau, Pierre Ledoux, Dmitry Rudnev, Alex E. Lash, Wataru Fujibuchi, Ron Edgar:
  NCBI GEO: mining millions of expression profiles - database and tools. 562-566
  Electronic Edition (link) BibTeX
• Motohiko Tanino, Marie-Anne Debily, Takuro Tamura, Teruyoshi Hishiki, Osamu Ogasawara, Katsuji Murakawa, Shoko Kawamoto, Kouichi Itoh, Shinya Watanabe, Sandro José de Souza, Sandrine Imbeaud, Esther Graudens, Eric Eveno, Phillip Hilton, Yukio Sudo, Janet Kelso, Kazuho Ikeo, Tadashi Imanishi, Takashi Gojobori, Charles Auffray, Winston Hide, Kousaku Okubo:
  The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. 567-572
  Electronic Edition (link) BibTeX
• Vishal Shah, Sriram Sridhar, Jennifer Beane, Jerome S. Brody, Avrum Spira:
  SIEGE: Smoking Induced Epithelial Gene Expression Database. 573-579
  Electronic Edition (link) BibTeX
• Catherine A. Ball, Ihab A. B. Awad, Janos Demeter, Jeremy Gollub, Joan M. Hebert, Tina Hernandez-Boussard, Heng Jin, John C. Matese, Michael Nitzberg, Farrell Wymore, Zachariah K. Zachariah, Patrick O. Brown, Gavin Sherlock:
  The Stanford Microarray Database accommodates additional microarray platforms and data formats. 580-582
  Electronic Edition (link) BibTeX
• Oliver Drews, Angelika Görg:
  DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels. 583-587
  Electronic Edition (link) BibTeX
• Florencio Pazos, David Guijas, Alfonso Valencia, Victor de Lorenzo:
  MetaRouter: bioinformatics for bioremediation. 588-592
  Electronic Edition (link) BibTeX
• Marie-Paule Lefranc, Véronique Giudicelli, Quentin Kaas, Elodie Duprat, Joumana Jabado-Michaloud, Dominique Scaviner, Chantal Ginestoux, Oliver Clément, Denys Chaume, Gérard Lefranc:
  IMGT, the international ImMunoGeneTics information system^®. 593-597
  Electronic Edition (link) BibTeX
• Nuwee Wiwatwattana, Anuj Kumar:
  Organelle DB: a cross-species database of protein localization and function. 598-604
  Electronic Edition (link) BibTeX
• Joshua L. Heazlewood, A. Harvey Millar:
  AMPDB: the Arabidopsis Mitochondrial Protein Database. 605-610
  Electronic Edition (link) BibTeX
• Marty C. Brandon, Marie T. Lott, Kevin Cuong Nguyen, Syawal Spolim, Shamkant B. Navathe, Pierre Baldi, Douglas C. Wallace:
  MITOMAP: a human mitochondrial genome database - 2004 update. 611-613
  Electronic Edition (link) BibTeX
• Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, Julie A. Dickerson:
  BarleyBase - an expression profiling database for plant genomics. 614-618
  Electronic Edition (link) BibTeX
• C. Künne, M. Lange, T. Funke, H. Miehe, T. Thiel, I. Grosse, U. Scholz:
  CR-EST: a resource for crop ESTs. 619-621
  Electronic Edition (link) BibTeX
• Stephen Rudd:
  openSputnik - a database to ESTablish comparative plant genomics using unsaturated sequence collections. 622-627
  Electronic Edition (link) BibTeX
• Stephen Rudd, Heiko Schoof, Klaus F. X. Mayer:
  PlantMarkers - a database of predicted molecular markers from plants. 628-632
  Electronic Edition (link) BibTeX
• John W. S. Brown, Peter J. Shaw, Paul Shaw, David F. Marshall:
  Arabidopsis nucleolar protein database (AtNoPDB). 633-636
  Electronic Edition (link) BibTeX
• Adam M. Gustafson, Edwards Allen, Scott A. Givan, Daniel Smith, James C. Carrington, Kristin D. Kasschau:
  ASRP: the Arabidopsis Small RNA Project Database. 637-640
  Electronic Edition (link) BibTeX
• Sébastien Aubourg, Véronique Brunaud, Clémence Bruyère, Mark Cock, Richard Cooke, Annick Cottet, Arnaud Couloux, Patrice Déhais, Gilbert Deléage, Aymeric Duclert, Manuel Echeverria, Aimée Eschbach, Denis Falconet, Ghislain Filippi, Christine Gaspin, Christophe Geourjon, Jean-Michel Grienenberger, Guy Houlné, Elisabeth Jamet, Frédéric Lechauve, Olivier Leleu, Philippe Leroy, Régis Mache, Christian Meyer, Hafed Nedjari, Ioan Negrutiu, Valérie Orsini, Eric Peyretaillade, Cyril Pommier, Jeroen Raes, Jean-Loup Risler, Stéphane Rivière, Stephane Rombauts, Pierre Rouzé, Michel Schneider, Philippe Schwob, Ian Small, Ghislain Soumayet-Kampetenga, Darko Stankovski, Claire Toffano, Mich