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    Databases in Molecular Biology (2003):

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

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

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

  • Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Francesco Nardone, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, and Robert Vaughan
    The EMBL Nucleotide Sequence Database: major new developments
    Nucleic Acids Res. 31: 17-22.

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

  • David L. Wheeler, Deanna M. Church, Scott Federhen, Alex E. Lash, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tatiana A. Tatusova, and Lukas Wagner
    Database resources of the National Center for Biotechnology
    Nucleic Acids Res. 31: 28-33.

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

  • M. Clamp, D. Andrews, D. Barker, P. Bevan, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, T. Hubbard, A. Kasprzyk, D. Keefe, H. Lehvaslaiho, V. Iyer, C. Melsopp, E. Mongin, R. Pettett, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik, and E. Birney
    Ensembl 2002: accommodating comparative genomics
    Nucleic Acids Res. 31: 38-42.

  • Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola Mulder, Claire O'Donovan, Helen Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, and Graham Cameron
    The European Bioinformatics Institute's data resources
    Nucleic Acids Res. 31: 43-50.

  • D. Karolchik, R. Baertsch, M. Diekhans, T. S. Furey, A. Hinrichs, Y. T. Lu, K. M. Roskin, M. Schwartz, C. W. Sugnet, D. J. Thomas, R. J. Weber, D. Haussler, and W. J. Kent
    The UCSC Genome Browser Database
    Nucleic Acids Res. 31: 51-54.

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

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

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

  • Alvis Brazma, Helen Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Jaak Vilo, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Philippe Rocca-Serra, and Susanna-Assunta Sansone
    ArrayExpress - a public repository for microarray gene expression data at the EBI
    Nucleic Acids Res. 31: 68-71.

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

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

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

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

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

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

  • Jeremy Gollub, Catherine A. Ball, Gail Binkley, Janos Demeter, David B. Finkelstein, Joan M. Hebert, Tina Hernandez-Boussard, Heng Jin, Miroslava Kaloper, John C. Matese, Mark Schroeder, Patrick O. Brown, David Botstein, and Gavin Sherlock
    The Stanford Microarray Database: data access and quality assessment tools
    Nucleic Acids Res. 31: 94-96.

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

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

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

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

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

  • Julia V. Ponomarenko, Tatyana I. Merkulova, Galina V. Orlova, Oleg N. Fokin, Elena V. Gorshkova, Anatoly S. Frolov, Vadim P. Valuev, and Mikhail P. Ponomarenko
    rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation
    Nucleic Acids Res. 31: 118-121.

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

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

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

  • Todd W. Harris, Raymond Lee, Erich Schwarz, Keith Bradnam, Daniel Lawson, Wen Chen, Darin Blasier, Eimear Kenny, Fiona Cunningham, Ranjana Kishore, Juancarlos Chan, Hans-Michael Muller, Andrei Petcherski, Gudmundur Thorisson, Allen Day, Tamberlyn Bieri, Anthony Rogers, Chao-Kung Chen, John Spieth, Paul Sternberg, Richard Durbin, and Lincoln D. Stein
    WormBase: a cross-species database for comparative genomics
    Nucleic Acids Res. 31: 133-137.

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

  • Marilyn Safran, Vered Chalifa-Caspi, Orit Shmueli, Tsviya Olender, Michal Lapidot, Naomi Rosen, Michael Shmoish, Yakov Peter, Gustavo Glusman, Ester Feldmesser, Avital Adato, Inga Peter, Miriam Khen, Tal Atarot, Yoram Groner, and Doron Lancet
    Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE
    Nucleic Acids Res. 31: 142-146.

  • Jeremy D. Glasner, Paul Liss, Guy Plunkett III, Aaron Darling, Tejasvini Prasad, Michael Rusch, Alexis Byrnes, Michael Gilson, Bryan Biehl, Frederick R. Blattner, and Nicole T. Perna
    ASAP, a systematic annotation package for community analysis of genomes
    Nucleic Acids Res. 31: 147-151.

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

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

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

  • Ross Overbeek, Niels Larsen, Theresa Walunas, Mark D'Souza, Gordon Pusch, Eugene Selkov, Jr, Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vasieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, and Nikos Kyrpides
    The ERGOTM genome analysis and discovery system
    Nucleic Acids Res. 31: 164-171.

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

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

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

  • David E. Matthews, Victoria L. Carollo, Gerard R. Lazo, and Olin D. Anderson
    GrainGenes, the genome database for small-grain crops
    Nucleic Acids Res. 31: 183-186.

    Ê

  • S. Garcia-Vallve, E. Guzman, M. A. Montero, and A. Romeu
    HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes
    Nucleic Acids Res. 31: 187-189.

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

  • Judith A. Blake, Joel E. Richardson, Carol J. Bult, Jim A. Kadin, and Janan T. Eppig
    MGD: the Mouse Genome Database
    Nucleic Acids Res. 31: 193-195.

    Ê

  • Anne-Franoise J. Lamblin, John A. Crow, James E. Johnson, Kevin A. T. Silverstein, Timothy M. Kunau, Alan Kilian, Diane Benz, Martina Stromvik, Gabriella EndrŽ, Kathryn A. VandenBosch, Douglas R. Cook, Nevin D. Young, and Ernest F. Retzel
    MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome
    Nucleic Acids Res. 31: 196-201.

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

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

  • Amit Bahl, Brian Brunk, Jonathan Crabtree, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant, Hagai Ginsburg, Dinesh Gupta, Jessica C. Kissinger, Philip Labo, Li Li, Matthew D. Mailman, Arthur J. Milgram, David S. Pearson, David S. Roos, Jonathan Schug, Christian J. Stoeckert, Jr, and Patricia Whetzel
    PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
    Nucleic Acids Res. 31: 212-215.

  • Shuai Weng, Qing Dong, Rama Balakrishnan, Karen Christie, Maria Costanzo, Kara Dolinski, Selina S. Dwight, Stacia Engel, Dianna G. Fisk, Eurie Hong, Laurie Issel-Tarver, Anand Sethuraman, Chandra Theesfeld, Rey Andrada, Gail Binkley, Christopher Lane, Mark Schroeder, David Botstein, and J. Michael Cherry
    Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins
    Nucleic Acids Res. 31: 216-218.

  • Maximilian Diehn, Gavin Sherlock, Gail Binkley, Heng Jin, John C. Matese, Tina Hernandez-Boussard, Christian A. Rees, J. Michael Cherry, David Botstein, Patrick O. Brown, and Ash A. Alizadeh
    SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
    Nucleic Acids Res. 31: 219-223.

  • Seung Yon Rhee, William Beavis, Tanya Z. Berardini, Guanghong Chen, David Dixon, Aisling Doyle, Margarita Garcia-Hernandez, Eva Huala, Gabriel Lander, Mary Montoya, Neil Miller, Lukas A. Mueller, Suparna Mundodi, Leonore Reiser, Julie Tacklind, Dan C. Weems, Yihe Wu, Iris Xu, Daniel Yoo, Jungwon Yoon, and Peifen Zhang
    The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
    Nucleic Acids Res. 31: 224-228.

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

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

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

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

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

  • Gary D. Bader, Doron Betel, and Christopher W. V. Hogue
    BIND: the Biomolecular Interaction Network Database
    Nucleic Acids Res. 31: 248-250.

    Ê

  • See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan, and Kui Lin
    InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes
    Nucleic Acids Res. 31: 251-254.

  • Z. L. Ji, X. Chen, C. J. Zhen, L. X. Yao, L. Y. Han, W. K. Yeo, P. C. Chung, H. S. Puy, Y. T. Tay, A. Muhammad, and Y. Z. Chen
    KDBI: Kinetic Data of Bio-molecular Interactions database
    Nucleic Acids Res. 31: 255-257.

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

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

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

  • H. Rajeevan, M. V. Osier, K.-H. Cheung, H. Deng, L. Druskin, R. Heinzen, J. R. Kidd, S. Stein, A. J. Pakstis, N. P. Tosches, C.-C. Yeh, P. L. Miller, and K. K. Kidd
    ALFRED: the ALelle FREquency Database. Update
    Nucleic Acids Res. 31: 270-271.

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

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

  • Doug Stryke, Michiko Kawamoto, Conrad C. Huang, Susan J. Johns, Leslie A. King, Courtney A. Harper, Elaine C. Meng, Roy E. Lee, Alice Yee, Larry L'Italien, Pao-Tien Chuang, Stephen G. Young, William C. Skarnes, Patricia C. Babbitt, and Thomas E. Ferrin
    BayGenomics: a resource of insertional mutations in mouse embryonic stem cells
    Nucleic Acids Res. 31: 278-281.

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

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

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

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

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

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

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

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

  • Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Phillip Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, and Evgueni M. Zdobnov
    The InterPro Database, 2003 brings increased coverage and new features
    Nucleic Acids Res. 31: 315-318.

    Ê

  • Markus Fischer and JŸrgen Pleiss
    The Lipase Engineering Database: a navigation and analysis tool for protein families
    Nucleic Acids Res. 31: 319-321.

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

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

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

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

  • Paul D. Thomas, Anish Kejariwal, Michael J. Campbell, Huaiyu Mi, Karen Diemer, Nan Guo, Istvan Ladunga, Betty Ulitsky-Lazareva, Anushya Muruganujan, Steven Rabkin, Jody A. Vandergriff, and Olivier Doremieux
    PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification
    Nucleic Acids Res. 31: 334-341.

  • Jason H. Tchieu, Fariba Fana, J. Lynn Fink, Jeffrey Harper, T. Murlidharan Nair, R. Hannes Niedner, Douglas W. Smith, Kenneth Steube, Tobey M. Tam, Stella Veretnik, Degeng Wang, and Michael Gribskov
    The PlantsP and PlantsT Functional Genomics Databases
    Nucleic Acids Res. 31: 342-344.

  • Cathy H. Wu, Lai-Su L. Yeh, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhangzhi Hu, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, C.R. Vinayaka, Jian Zhang, and Winona C. Barker
    The Protein Information Resource
    Nucleic Acids Res. 31: 345-347.

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

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

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

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

  • Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-Claude Blatter, Anne Estreicher, Elisabeth Gasteiger, Maria J. Martin, Karine Michoud, Claire O'Donovan, Isabelle Phan, Sandrine Pilbout, and Michel Schneider
    The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    Nucleic Acids Res. 31: 365-370.

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

  • V. Matys, E. Fricke, R. Geffers, E. Gš§ling, M. Haubrock, R. Hehl, K. Hornischer, D. Karas, A. E. Kel, O. V. Kel-Margoulis, D.-U. Kloos, S. Land, B. Lewicki-Potapov, H. Michael, R. MŸnch, I. Reuter, S. Rotert, H. Saxel, M. Scheer, S. Thiele, and E. Wingender
    TRANSFAC¨: transcriptional regulation, from patterns to profiles
    Nucleic Acids Res. 31: 374-378.

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

  • Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Anna R. Panchenko, Bachoti S. Rao, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, and Stephen H. Bryant
    CDD: a curated Entrez database of conserved domain alignments
    Nucleic Acids Res. 31: 383-387.

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

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

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

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

  • T. K. Attwood, P. Bradley, D. R. Flower, A. Gaulton, N. Maudling, A. L. Mitchell, G. Moulton, A. Nordle, K. Paine, P. Taylor, A. Uddin, and C. Zygouri
    PRINTS and its automatic supplement, prePRINTS
    Nucleic Acids Res. 31: 400-402.

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

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

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

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

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

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

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

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

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

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

    Ê

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

    Ê

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

  • J. R. Cole, B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje
    The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
    Nucleic Acids Res. 31: 442-443.

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

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

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

  • F. M. G. Pearl, C. F. Bennett, J. E. Bray, A. P. Harrison, N. Martin, A. Shepherd, I. Sillitoe, J. Thornton, and C. A. Orengo
    The CATH database: an extended protein family resource for structural and functional genomics
    Nucleic Acids Res. 31: 452-455.

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

  • H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel, P. McNeil, A. Naim, R. Newman, T. Oldfield, J. Pineda, A. Rachedi, J. Copeland, A. Sitnov, S. Sobhany, A. Suarez-Uruena, J. Swaminathan, M. Tagari, J. Tate, S. Tromm, S. Velankar, and W. Vranken
    E-MSD: the European Bioinformatics Institute Macromolecular Structure Database
    Nucleic Acids Res. 31: 458-462.

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

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

  • Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, and Stephen H. Bryant
    MMDB: Entrez's 3D-structure database
    Nucleic Acids Res. 31: 474-477.

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

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

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

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

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

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

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

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

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

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

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

 

>Latest update: April 10, 2003


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