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    Databases in Molecular Biology (2005):

    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 2005:

  • Michael Y. Galperin
    The Molecular Biology Database Collection: 2005 update
    Nucl. Acids Res. 33: D5-D24 Database Listing

  • Y. Tateno, N. Saitou, K. Okubo, H. Sugawara, and T. Gojobori
    DDBJ in collaboration with mass-sequencing teams on annotation
    Nucl. Acids Res. 33: D25-D28

  • 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, and Rolf Apweiler
    The EMBL Nucleotide Sequence Database
    Nucl. Acids Res. 33: D29-D33

  • Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
    GenBank
    Nucl. Acids Res. 33: D34-D38

  • 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 Tatusov, Tatiana A. Tatusova, Lukas Wagner, and Eugene Yaschenko
    Database resources of the National Center for Biotechnology Information
    Nucl. Acids Res. 33: D39-D45

  • Catherine Brooksbank, Graham Cameron, and Janet Thornton
    The European Bioinformatics Institute's data resources: towards systems biology
    Nucl. Acids Res. 33: D46-D53

  • Donna Maglott, Jim Ostell, Kim D. Pruitt, and Tatiana Tatusova
    Entrez Gene: gene-centered information at NCBI
    Nucl. Acids Res. 33: D54-D58

  • Khelifi Adel, Duret Laurent, and Mouchiroud Dominique
    HOPPSIGEN: a database of human and mouse processed pseudogenes
    Nucl. Acids Res. 33: D59-D66

  • Victor G. Levitsky, Aleksey V. Katokhin, Olga A. Podkolodnaya, Dagmara P. Furman, and Nikolay A. Kolchanov
    NPRD: Nucleosome Positioning Region Database
    Nucl. Acids Res. 33: D67-D70

  • Y. Lee, J. Tsai, S. Sunkara, S. Karamycheva, G. Pertea, R. Sultana, V. Antonescu, A. Chan, F. Cheung, and J. Quackenbush
    The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes
    Nucl. Acids Res. 33: D71-D74

  • Pora Kim, Namshin Kim, Younghee Lee, Bumjin Kim, Youngah Shin, and Sanghyuk Lee
    ECgene: genome annotation for alternative splicing
    Nucl. Acids Res. 33: D75-D79

  • Hsien-Da Huang, Jorng-Tzong Horng, Feng-Mao Lin, Yu-Chung Chang, and Chen-Chia Huang
    SpliceInfo: an information repository for mRNA alternative splicing in human genome
    Nucl. Acids Res. 33: D80-D85

  • Endre Barta, Endre Sebestyén, Tamás B. Pálfy, Gábor Tóth, Csaba P. Ortutay, and László Patthy
    DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
    Nucl. Acids Res. 33: D86-D90

  • Voichita D. Marinescu, Isaac S. Kohane, and Alberto Riva
    The MAPPER database: a multi-genome catalog of putative transcription factor binding sites
    Nucl. Acids Res. 33: D91-D97

  • Abel D. González, Vladimir Espinosa, Ana T. Vasconcelos, Ernesto Pérez-Rueda, and Julio Collado-Vides
    TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes
    Nucl. Acids Res. 33: D98-D102

  • Fang Zhao, Zhenyu Xuan, Lihua Liu, and Michael Q. Zhang
    TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies
    Nucl. Acids Res. 33: D103-D107

  • Matthias Truss, Maciej Swat, Szymon M. Kielbasa, Reinhold Schäfer, Hanspeter Herzel, and 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
    Nucl. Acids Res. 33: D108-D111

  • Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, and Runsheng Chen
    NONCODE: an integrated knowledge database of non-coding RNAs
    Nucl. Acids Res. 33: D112-D115

  • Haibo Zhang, Jun Hu, Michael Recce, and Bin Tian
    PolyA_DB: a database for mammalian mRNA polyadenylation
    Nucl. Acids Res. 33: D116-D120

  • Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, and Alex Bateman
    Rfam: annotating non-coding RNAs in complete genomes
    Nucl. Acids Res. 33: D121-D124

  • Ken C. Pang, Stuart Stephen, Pär G. Engström, Khairina Tajul-Arifin, Weisan Chen, Claes Wahlestedt, Boris Lenhard, Yoshihide Hayashizaki, and John S. Mattick
    RNAdb—a comprehensive mammalian noncoding RNA database
    Nucl. Acids Res. 33: D125-D130

  • Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, and Erik L. L. Sonnhammer
    siRNAdb: a database of siRNA sequences
    Nucl. Acids Res. 33: D131-D134

  • James A. McCloskey and Jef Rozenski
    The Small Subunit rRNA Modification Database
    Nucl. Acids Res. 33: D135-D138

  • Mathias Sprinzl and Konstantin S. Vassilenko
    Compilation of tRNA sequences and sequences of tRNA genes
    Nucl. Acids Res. 33: D139-D140

  • Flavio Mignone, Giorgio Grillo, Flavio Licciulli, Michele Iacono, Sabino Liuni, Paul J. Kersey, Jorge Duarte, Cecilia Saccone, and Graziano Pesole
    UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
    Nucl. Acids Res. 33: D141-D146

  • Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, and Nicholas Lamb
    PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
    Nucl. Acids Res. 33: D147-D153

  • Amos Bairoch, Rolf Apweiler, 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 O'Donovan, Nicole Redaschi, and Lai-Su L. Yeh
    The Universal Protein Resource (UniProt)
    Nucl. Acids Res. 33: D154-D159

  • Sven Mika and Burkhard Rost
    NMPdb: Database of Nuclear Matrix Proteins
    Nucl. Acids Res. 33: D160-D163

  • Sébastien Rey, Michael Acab, Jennifer L. Gardy, Matthew R. Laird, Katalin deFays, Christophe Lambert, and Fiona S. L. Brinkman
    PSORTdb: a protein subcellular localization database for bacteria
    Nucl. Acids Res. 33: D164-D168

  • Yunjia Chen, Yong Zhang, Yanbin Yin, Ge Gao, Songgang Li, Ying Jiang, Xiaocheng Gu, and Jingchu Luo
    SPD—a web-based secreted protein database
    Nucl. Acids Res. 33: D169-D173

  • Ya-Hui Chang, Wen-Hui Su, Tso-Ching Lee, Hsiao-Fang Sunny Sun, Chia-Hsiang Chen, Wen-Harn Pan, Shih-Feng Tsai, and Yuh-Shan Jou
    TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations
    Nucl. Acids Res. 33: D174-D177

  • Qiaojuan Jane Su, Lin Lu, Serge Saxonov, and Douglas L. Brutlag
    eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity
    Nucl. Acids Res. 33: D178-D182

  • Vladimir A. Ivanisenko, Sergey S. Pintus, Dmitry A. Grigorovich, and Nickolay A. Kolchanov
    PDBSite: a database of the 3D structure of protein functional sites
    Nucl. Acids Res. 33: D183-D187

  • Andreas Heger, Christopher Andrew Wilton, Ashwin Sivakumar, and Liisa Holm
    ADDA: a domain database with global coverage of the protein universe
    Nucl. Acids Res. 33: D188-D191

  • 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, and Stephen H. Bryant
    CDD: a Conserved Domain Database for protein classification
    Nucl. Acids Res. 33: D192-D196

  • Saraswathi Abhiman and Erik L. L. Sonnhammer
    FunShift: a database of function shift analysis on protein subfamilies
    Nucl. Acids Res. 33: D197-D200

  • Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel 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 Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, and Cathy H. Wu
    InterPro, progress and status in 2005
    Nucl. Acids Res. 33: D201-D205

  • Shu-Hsien Sheu, David R. Lancia, Jr, Karl H. Clodfelter, Melissa R. Landon, and Sandor Vajda
    PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes
    Nucl. Acids Res. 33: D206-D211

  • Catherine Bru, Emmanuel Courcelle, Sébastien Carrère, Yoann Beausse, Sandrine Dalmar, and Daniel Kahn
    The ProDom database of protein domain families: more emphasis on 3D
    Nucl. Acids Res. 33: D212-D215

  • Noam Kaplan, Ori Sasson, Uri Inbar, Moriah Friedlich, Menachem Fromer, Hillel Fleischer, Elon Portugaly, Nathan Linial, and Michal Linial
    ProtoNet 4.0: A hierarchical classification of one million protein sequences
    Nucl. Acids Res. 33: D216-D218

  • James Casbon and Mansoor A. S. Saqi
    S4: structure-based sequence alignments of SCOP superfamilies
    Nucl. Acids Res. 33: D219-D222

  • Kristian Vlahovicek, László Kaján, Vilmos Ágoston, and Sándor Pongor
    The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines
    Nucl. Acids Res. 33: D223-D225

  • Thomas Meinel, Antje Krause, Hannes Luz, Martin Vingron, and Eike Staub
    The SYSTERS Protein Family Database in 2005
    Nucl. Acids Res. 33: D226-D229

  • Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis
    REBASE—restriction enzymes and DNA methyltransferases
    Nucl. Acids Res. 33: D230-D232

  • Nita Deshpande, Kenneth J. Addess, Wolfgang F. 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 Westbrook, Helen M. Berman, and Philip E. Bourne
    The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema
    Nucl. Acids Res. 33: D233-D237

  • Jae-Min Shin and Doo-Ho Cho
    PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures
    Nucl. Acids Res. 33: D238-D241

  • Thomas Lütteke, Martin Frank, and Claus-W. von der Lieth
    Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB
    Nucl. Acids Res. 33: D242-D246

  • Frances Pearl, Annabel Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony Lewis, Christopher Bennett, Russell Marsden, Alistair Grant, David Lee, Adrian Akpor, Michael Maibaum, Andrew Harrison, Timothy Dallman, Gabrielle Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline Johnston, Antonio Sillero, Janet Thornton, and Christine Orengo
    The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
    Nucl. Acids Res. 33: D247-D251

  • Ganesan Pugalenthi, Anirban Bhaduri, and Ramanathan Sowdhamini
    GenDiS: Genomic Distribution of protein structural domain Superfamilies
    Nucl. Acids Res. 33: D252-D255

  • Véronique Giudicelli, Denys Chaume, and Marie-Paule Lefranc
    IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes
    Nucl. Acids Res. 33: D256-D261

  • S. Velankar, P. McNeil, V. Mittard-Runte, A. Suarez, D. Barrell, R. Apweiler, and K. Henrick
    E-MSD: an integrated data resource for bioinformatics
    Nucl. Acids Res. 33: D262-D265

  • Roman A. Laskowski, Victor V. Chistyakov, and Janet M. Thornton
    PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids
    Nucl. Acids Res. 33: D266-D268

  • 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, and 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
    Nucl. Acids Res. 33: D269-D274

  • Gábor E. Tusnády, Zsuzsanna Dosztányi, and István Simon
    PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank
    Nucl. Acids Res. 33: D275-D278

  • Kate F. Fulton, Glyn L. Devlin, Rachel A. Jodun, Linda Silvestri, Stephen P. Bottomley, Alan R. Fersht, and Ashley M. Buckle
    PFD: a database for the investigation of protein folding kinetics and stability
    Nucl. Acids Res. 33: D279-D283

  • Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano, and Paul D. Thomas
    The PANTHER database of protein families, subfamilies, functions and pathways
    Nucl. Acids Res. 33: D284-D288

  • Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, and Russ B. Altman
    Biomedical term mapping databases
    Nucl. Acids Res. 33: D289-D293

  • J. R. Cole, B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity, and J. M. Tiedje
    The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
    Nucl. Acids Res. 33: D294-D296

  • 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, and Rolf Apweiler
    Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
    Nucl. Acids Res. 33: D297-D302

  • José M. Peregrín-Alvarez, Andrew Yam, Gaya Sivakumar, and John Parkinson
    PartiGeneDB—collating partial genomes
    Nucl. Acids Res. 33: D303-D307

  • M. Louise Riley, Thorsten Schmidt, Christian Wagner, Hans-Werner Mewes, and Dmitrij Frishman
    The PEDANT genome database in 2005
    Nucl. Acids Res. 33: D308-D310

  • Elliot J. Lefkowitz, Chris Upton, Shankar S. Changayil, Charles Buck, Paula Traktman, and R. Mark L. Buller
    Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource
    Nucl. Acids Res. 33: D311-D316

  • Paul Stothard, Gary Van Domselaar, Savita Shrivastava, Anchi Guo, Brian O'Neill, Joseph Cruz, Michael Ellison, and David S. Wishart
    BacMap: an interactive picture atlas of annotated bacterial genomes
    Nucl. Acids Res. 33: D317-D320

  • Hiroyuki Ogata and Jean-Michel Claverie
    Metagrowth: a new resource for the building of metabolic hypotheses in microbiology
    Nucl. Acids Res. 33: D321-D324

  • Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, and Qi Jin
    VFDB: a reference database for bacterial virulence factors
    Nucl. Acids Res. 33: D325-D328

  • Raju V. Misra, Richard S. P. Horler, Wolfgang Reindl, Igor I. Goryanin, and Gavin H. Thomas
    EchoBASE: an integrated post-genomic database for Escherichia coli
    Nucl. Acids Res. 33: D329-D333

  • Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne Paley, Ian T. Paulsen, Martín Peralta-Gil, and Peter D. Karp
    EcoCyc: a comprehensive database resource for Escherichia coli
    Nucl. Acids Res. 33: D334-D337

  • Geoffrey L. Winsor, Raymond Lo, Shannan J. Ho Sui, Korine S.E. Ung, Shaoshan Huang, Dean Cheng, Wai-Kay Ho Ching, Robert E. W. Hancock, and Fiona S. L. Brinkman
    Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation
    Nucl. Acids Res. 33: D338-D343

  • Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy, K. R. Rajyashri, Villoo Morawala Patell, and Chris Bowler
    The Diatom EST Database
    Nucl. Acids Res. 33: D344-D347

  • Leandro Hermida, Sophie Brachat, Sylvia Voegeli, Peter Philippsen, and Michael Primig
    The Ashbya Genome Database (AGD)—a tool for the yeast community and genome biologists
    Nucl. Acids Res. 33: D348-D352

  • C. d'Enfert, S. Goyard, S. Rodriguez-Arnaveilhe, L. Frangeul, L. Jones, F. 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, and A. J. P. Brown
    CandidaDB: a genome database for Candida albicans pathogenomics
    Nucl. Acids Res. 33: D353-D357

  • Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Gail Binkley, Christopher Lane, Stuart R. Miyasato, and Gavin Sherlock
    The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information
    Nucl. Acids Res. 33: D358-D363

  • U. Güldener, M. Münsterkötter, G. Kastenmüller, N. Strack, J. van Helden, C. Lemer, J. Richelles, S. J. Wodak, J. García-Martínez, J. E. Pérez-Ortín, H. Michael, A. Kaps, E. Talla, B. Dujon, B. André, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, and H. W. Mewes
    CYGD: the Comprehensive Yeast Genome Database
    Nucl. Acids Res. 33: D364-D368

  • Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Ilona Pylvänäinen, Graham J. L. Kemp, Olle Nerman, and Anders Blomberg
    PROPHECY—a database for high-resolution phenomics
    Nucl. Acids Res. 33: D369-D373

  • 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 Nash, Rose Oughtred, Marek Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Anand Sethuraman, Shuai Weng, David Botstein, and J. Michael Cherry
    Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)
    Nucl. Acids Res. 33: D374-D377

  • Michael Riffle, Lars Malmström, and Trisha N. Davis
    The Yeast Resource Center Public Data Repository
    Nucl. Acids Res. 33: D378-D382

  • 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 Muller, 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, and Lincoln D. Stein
    WormBase: a comprehensive data resource for Caenorhabditis biology and genomics
    Nucl. Acids Res. 33: D383-D389

  • Rachel A. Drysdale, Madeline A. Crosby, and The FlyBase Consortium
    FlyBase: genes and gene models
    Nucl. Acids Res. 33: D390-D395

  • Andre R. O. Cavalcanti, Thomas H. Clarke, and Laura F. Landweber
    MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates
    Nucl. Acids Res. 33: D396-D398

  • 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, and Jun Yu
    SilkDB: a knowledgebase for silkworm biology and genomics
    Nucl. Acids Res. 33: D399-D402

  • M. D. Prasad, M. Muthulakshmi, K. P. Arunkumar, M. Madhu, V. B. Sreenu, V. Pavithra, B. Bose, H. A. Nagarajaram, K. Mita, T. Shimada, and J. Nagaraju
    SilkSatDb: a microsatellite database of the silkworm, Bombyx mori
    Nucl. Acids Res. 33: D403-D406

  • Nozomi Nagano
    EzCatDB: the Enzyme Catalytic-mechanism Database
    Nucl. Acids Res. 33: D407-D412

  • Amelie Stein, Robert B. Russell, and Patrick Aloy
    3did: interacting protein domains of known three-dimensional structure
    Nucl. Acids Res. 33: D413-D417

  • C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, M. Bajec, K. Bantoft, D. Betel, B. Bobechko, K. Boutilier, E. Burgess, K. Buzadzija, R. Cavero, C. D'Abreo, I. Donaldson, D. Dorairajoo, M. J. Dumontier, M. R. Dumontier, V. Earles, R. Farrall, H. Feldman, E. Garderman, Y. Gong, R. Gonzaga, V. Grytsan, E. Gryz, V. Gu, E. Haldorsen, A. Halupa, R. Haw, A. Hrvojic, L. Hurrell, R. 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, G. Pintilie, R. Pirone, J. J. Salama, S. Sgro, T. Shan, Y. Shu, J. Siew, D. Skinner, K. Snyder, R. Stasiuk, D. Strumpf, B. Tuekam, S. Tao, Z. Wang, M. White, R. Willis, C. Wolting, S. Wong, A. Wrong, C. Xin, R. Yao, B. Yates, S. Zhang, K. Zheng, T. Pawson, B. F. F. Ouellette, and C. W. V. Hogue
    The Biomolecular Interaction Network Database and related tools 2005 update
    Nucl. Acids Res. 33: D418-D424

  • E. A. Ananko, N. L. Podkolodny, I. L. Stepanenko, O. A. Podkolodnaya, D. A. Rasskazov, D. S. Miginsky, V. A. Likhoshvai, A. V. Ratushny, N. N. Podkolodnaya, and N. A. Kolchanov
    GeneNet in 2005
    Nucl. Acids Res. 33: D425-D427

  • G. Joshi-Tope, M. Gillespie, I. Vastrik, P. D'Eustachio, E. Schmidt, B. de Bono, B. Jassal, G.R. Gopinath, G.R. Wu, L. Matthews, S. Lewis, E. Birney, and L. Stein
    Reactome: a knowledgebase of biological pathways
    Nucl. Acids Res. 33: D428-D432

  • Christian von Mering, Lars J. Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, and Peer Bork
    STRING: known and predicted protein–protein associations, integrated and transferred across organisms
    Nucl. Acids Res. 33: D433-D437

  • 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, and Jun Wang
    ChickVD: a sequence variation database for the chicken genome
    Nucl. Acids Res. 33: D438-D441

  • Vamsi Veeramachaneni and Wojciech Makalowski
    DED: Database of Evolutionary Distances
    Nucl. Acids Res. 33: D442-D446

  • T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and E. Birney
    Ensembl 2005
    Nucl. Acids Res. 33: D447-D453

  • Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, and W. James Kent
    The UCSC Proteome Browser
    Nucl. Acids Res. 33: D454-D458

  • J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, P. Meidl, S. M. Searle, J. Stalker, R. Storey, S. Trevanion, L. Wilming, and T. Hubbard
    The Vertebrate Genome Annotation (Vega) database
    Nucl. Acids Res. 33: D459-D465

  • Laura Elnitski, Belinda Giardine, Prachi Shah, Yi Zhang, Cathy Riemer, Matthew Weirauch, Richard Burhans, Webb Miller, and Ross C. Hardison
    Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results
    Nucl. Acids Res. 33: D466-D470

  • Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, and the Mouse Genome Database Group
    The Mouse Genome Database (MGD): from genes to mice—a community resource for mouse biology
    Nucl. Acids Res. 33: D471-D475

  • Kevin P. O'Brien, Maido Remm, and Erik L. L. Sonnhammer
    Inparanoid: a comprehensive database of eukaryotic orthologs
    Nucl. Acids Res. 33: D476-D480

  • Eric Bazin, Laurent Duret, Simon Penel, and Nicolas Galtier
    Polymorphix: a sequence polymorphism database
    Nucl. Acids Res. 33: D481-D484

  • Norberto de la Cruz, Susan Bromberg, Dean Pasko, Mary Shimoyama, Simon 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 Kwitek, Peter Tonellato, and Howard Jacob
    The Rat Genome Database (RGD): developments towards a phenome database
    Nucl. Acids Res. 33: D485-D491

  • Greta Petersen, Per Johnson, Lars Andersson, Karin Klinga-Levan, Pedro M. Gómez-Fabre, and Fredrik StĆhl
    RatMap—rat genome tools and data
    Nucl. Acids Res. 33: D492-D494

  • Christian Roth, Matthew J. Betts, Pär Steffansson, Gisle Sœlensminde, and David A. Liberles
    The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics
    Nucl. Acids Res. 33: D495-D497

  • Tobias Penzkofer, Thomas Dandekar, and Tomasz Zemojtel
    L1Base: from functional annotation to prediction of active LINE-1 elements
    Nucl. Acids Res. 33: D498-D500

  • Kim D. Pruitt, Tatiana Tatusova, and Donna R. Maglott
    NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
    Nucl. Acids Res. 33: D501-D504

  • Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, and Sandro Banfi
    DG-CST (Disease Gene Conserved Sequence Tags), a database of human–mouse conserved elements associated to disease genes
    Nucl. Acids Res. 33: D505-D510

  • Robert Hoffmann, Joaquin Dopazo, Juan C. Cigudosa, and Alfonso Valencia
    HCAD, closing the gap between breakpoints and genes
    Nucl. Acids Res. 33: D511-D513

  • Ada Hamosh, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, and Victor A. McKusick
    Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
    Nucl. Acids Res. 33: D514-D517

  • Hyo Jin Kang, Kyoung Oak Choi, Byung-Dong Kim, Sangsoo Kim, and Young Joo Kim
    FESD: a Functional Element SNPs Database in human
    Nucl. Acids Res. 33: D518-D522

  • James Robinson, Matthew J. Waller, Peter Stoehr, and Steven G. E. Marsh
    IPD—the Immuno Polymorphism Database
    Nucl. Acids Res. 33: D523-D526

  • Joke Reumers, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Francois Stricher, Luis Serrano, and Frederic Rousseau
    SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs
    Nucl. Acids Res. 33: D527-D532

  • Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, and Kenta Nakai
    Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues
    Nucl. Acids Res. 33: D533-D536

  • João Pedro de Magalhães, Joana Costa, and Olivier Toussaint
    HAGR: the Human Ageing Genomic Resources
    Nucl. Acids Res. 33: D537-D543

  • 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, and Nathan Goodman
    T1DBase, a community web-based resource for type 1 diabetes research
    Nucl. Acids Res. 33: D544-D549

  • Yasuhiro Kasai, Shin-ichi Hashimoto, Tomoyuki Yamada, Jun Sese, Sumio Sugano, Kouji Matsushima, and Shinichi Morishita
    5'SAGE: 5'-end Serial Analysis of Gene Expression database
    Nucl. Acids Res. 33: D550-D552

  • H. Parkinson, U. Sarkans, M. Shojatalab, N. Abeygunawardena, S. Contrino, R. Coulson, A. Farne, G. Garcia Lara, E. Holloway, M. Kapushesky, P. Lilja, G. Mukherjee, A. Oezcimen, T. Rayner, P. Rocca-Serra, A. Sharma, S. Sansone, and A. Brazma
    ArrayExpress—a public repository for microarray gene expression data at the EBI
    Nucl. Acids Res. 33: D553-D555

  • Maxim Shklar, Liora Strichman-Almashanu, Orit Shmueli, Michael Shmoish, Marilyn Safran, and Doron Lancet
    GeneTide—Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases
    Nucl. Acids Res. 33: D556-D561

  • Tanya Barrett, Tugba O. Suzek, Dennis B. Troup, Stephen E. Wilhite, Wing-Chi Ngau, Pierre Ledoux, Dmitry Rudnev, Alex E. Lash, Wataru Fujibuchi, and Ron Edgar
    NCBI GEO: mining millions of expression profiles—database and tools
    Nucl. Acids Res. 33: D562-D566

  • 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, and Kousaku Okubo
    The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms
    Nucl. Acids Res. 33: D567-D572

  • Vishal Shah, Sriram Sridhar, Jennifer Beane, Jerome S. Brody, and Avrum Spira
    SIEGE: Smoking Induced Epithelial Gene Expression Database
    Nucl. Acids Res. 33: D573-D579

  • 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, and Gavin Sherlock
    The Stanford Microarray Database accommodates additional microarray platforms and data formats
    Nucl. Acids Res. 33: D580-D582

  • Oliver Drews and Angelika Görg
    DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels
    Nucl. Acids Res. 33: D583-D587

  • Florencio Pazos, David Guijas, Alfonso Valencia, and Victor De Lorenzo
    MetaRouter: bioinformatics for bioremediation
    Nucl. Acids Res. 33: D588-D592

  • Marie-Paule Lefranc, Véronique Giudicelli, Quentin Kaas, Elodie Duprat, Joumana Jabado-Michaloud, Dominique Scaviner, Chantal Ginestoux, Oliver Clément, Denys Chaume, and Gérard Lefranc
    IMGT, the international ImMunoGeneTics information system®
    Nucl. Acids Res. 33: D593-D597

  • Nuwee Wiwatwattana and Anuj Kumar
    Organelle DB: a cross-species database of protein localization and function
    Nucl. Acids Res. 33: D598-D604

  • Joshua L. Heazlewood and A. Harvey Millar
    AMPDB: the Arabidopsis Mitochondrial Protein Database
    Nucl. Acids Res. 33: D605-D610

  • Marty C. Brandon, Marie T. Lott, Kevin Cuong Nguyen, Syawal Spolim, Shamkant B. Navathe, Pierre Baldi, and Douglas C. Wallace
    MITOMAP: a human mitochondrial genome database—2004 update
    Nucl. Acids Res. 33: D611-D613

  • Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, and Julie A. Dickerson
    BarleyBase—an expression profiling database for plant genomics
    Nucl. Acids Res. 33: D614-D618

  • C. Künne, M. Lange, T. Funke, H. Miehe, T. Thiel, I. Grosse, and U. Scholz
    CR-EST: a resource for crop ESTs
    Nucl. Acids Res. 33: D619-D621

  • Stephen Rudd
    openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections
    Nucl. Acids Res. 33: D622-D627

  • Stephen Rudd, Heiko Schoof, and Klaus Mayer
    PlantMarkers—a database of predicted molecular markers from plants
    Nucl. Acids Res. 33: D628-D632

  • John W. S. Brown, Peter J. Shaw, Paul Shaw, and David F. Marshall
    Arabidopsis nucleolar protein database (AtNoPDB)
    Nucl. Acids Res. 33: D633-D636

  • Adam M. Gustafson, Edwards Allen, Scott Givan, Daniel Smith, James C. Carrington, and Kristin D. Kasschau
    ASRP: the Arabidopsis Small RNA Project Database
    Nucl. Acids Res. 33: D637-D640

  • 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, Stéphane Rombauts, Pierre Rouzé, Michel Schneider, Philippe Schwob, Ian Small, Ghislain Soumayet-Kampetenga, Darko Stankovski, Claire Toffano, Michael Tognolli, Michel Caboche, and Alain Lecharny
    GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts
    Nucl. Acids Res. 33: D641-D646

  • Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Motoaki Seki, Takashi Kuromori, Takuya Ito, Akihiko Konagaya, Tetsuro Toyoda, and Kazuo Shinozaki
    RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome
    Nucl. Acids Res. 33: D647-D650

  • Yuichi Ito, Kohji Arikawa, Baltazar A. Antonio, Isamu Ohta, Shinji Naito, Yoshiyuki Mukai, Atsuko Shimano, Masatoshi Masukawa, Michie Shibata, Mayu Yamamoto, Yukiyo Ito, Junri Yokoyama, Yasumichi Sakai, Katsumi Sakata, Yoshiaki Nagamura, Nobukazu Namiki, Takashi Matsumoto, Kenichi Higo, and Takuji Sasaki
    Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics
    Nucl. Acids Res. 33: D651-D655

  • Christopher G. Love, Andrew J. Robinson, Geraldine A. C. Lim, Clare J. Hopkins, Jacqueline Batley, Gary Barker, German C. Spangenberg, and David Edwards
    Brassica ASTRA: an integrated database for Brassica genomic research
    Nucl. Acids Res. 33: D656-D659

  • Michael D. Gonzales, Eric Archuleta, Andrew Farmer, Kamal Gajendran, David Grant, Randy Shoemaker, William D. Beavis, and Mark E. Waugh
    The Legume Information System (LIS): an integrated information resource for comparative legume biology
    Nucl. Acids Res. 33: D660-D665

  • Svenja Meyer, Axel Nagel, and Christiane Gebhardt
    PoMaMo—a comprehensive database for potato genome data
    Nucl. Acids Res. 33: D666-D670

  • Ida Retter, Hans Helmar Althaus, Richard Münch, and Werner Müller
    VBASE2, an integrative V gene database
    Nucl. Acids Res. 33: D671-D674

  • Susie M. Stephens, Jake Y. Chen, Marcel G. Davidson, Shiby Thomas, and Barry M. Trute
    Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences
    Nucl. Acids Res. 33: D675-D679

 

Latest update: August 4, 2005


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