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Volume 31(1);  January 1, 2003
Articles
Editorial
Nucleic Acids Res. 2003 January 1; 31(1): 0.
PMCID: PMC167138
The Molecular Biology Database Collection: 2003 update
Andreas D. Baxevanis
Nucleic Acids Res. 2003 January 1; 31(1): 1–12.
PMCID: PMC165567
DNA Data Bank of Japan (DDBJ) in XML
S. Miyazaki, H. Sugawara, T. Gojobori, and Y. Tateno
Nucleic Acids Res. 2003 January 1; 31(1): 13–16.
PMCID: PMC165535
The EMBL Nucleotide Sequence Database: major new developments
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
Nucleic Acids Res. 2003 January 1; 31(1): 17–22.
PMCID: PMC165468
GenBank
Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
Nucleic Acids Res. 2003 January 1; 31(1): 23–27.
PMCID: PMC165504
Database resources of the National Center for Biotechnology
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
Nucleic Acids Res. 2003 January 1; 31(1): 28–33.
PMCID: PMC165480
NCBI Reference Sequence Project: update and current status
Kim D. Pruitt, Tatiana Tatusova, and Donna R. Maglott
Nucleic Acids Res. 2003 January 1; 31(1): 34–37.
PMCID: PMC165558
Ensembl 2002: accommodating comparative genomics
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
Nucleic Acids Res. 2003 January 1; 31(1): 38–42.
PMCID: PMC165530
The European Bioinformatics Institute's data resources
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
Nucleic Acids Res. 2003 January 1; 31(1): 43–50.
PMCID: PMC165513
The UCSC Genome Browser Database
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
Nucleic Acids Res. 2003 January 1; 31(1): 51–54.
PMCID: PMC165576
CORG: a database for COmparative Regulatory Genomics
C. Dieterich, H. Wang, K. Rateitschak, H. Luz, and M. Vingron
Nucleic Acids Res. 2003 January 1; 31(1): 55–57.
PMCID: PMC165454
MBGD: microbial genome database for comparative analysis
Ikuo Uchiyama
Nucleic Acids Res. 2003 January 1; 31(1): 58–62.
PMCID: PMC165556
ParaDB: a tool for paralogy mapping in vertebrate genomes
Magalie Leveugle, Karine Prat, Nadine Perrier, Daniel Birnbaum, and François Coulier
Nucleic Acids Res. 2003 January 1; 31(1): 63–67.
PMCID: PMC165553
ArrayExpress—a public repository for microarray gene expression data at the EBI
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
Nucleic Acids Res. 2003 January 1; 31(1): 68–71.
PMCID: PMC165538
MEPD: a Medaka gene expression pattern database
Thorsten Henrich, Mirana Ramialison, Rebecca Quiring, Beate Wittbrodt, Makoto Furutani-Seiki, Joachim Wittbrodt, and Hisato Kondoh
Nucleic Acids Res. 2003 January 1; 31(1): 72–74.
PMCID: PMC165464
An improved version of the DNA methylation database (MethDB)
Céline Amoreira, Winfried Hindermann, and Christoph Grunau
Nucleic Acids Res. 2003 January 1; 31(1): 75–77.
PMCID: PMC165540
MTID: a database of Sleeping Beauty transposon insertions in mice
Kevin Roberg-Perez, Corey M. Carlson, and David A. Largaespada
Nucleic Acids Res. 2003 January 1; 31(1): 78–81.
PMCID: PMC165492
NetAffx: Affymetrix probesets and annotations
Guoying Liu, Ann E. Loraine, Ron Shigeta, Melissa Cline, Jill Cheng, Venu Valmeekam, Shaw Sun, David Kulp, and Michael A. Siani-Rose
Nucleic Acids Res. 2003 January 1; 31(1): 82–86.
PMCID: PMC165568
RECODE 2003
Pavel V. Baranov, Olga L. Gurvich, Andrew W. Hammer, Raymond F. Gesteland, and John F. Atkins
Nucleic Acids Res. 2003 January 1; 31(1): 87–89.
PMCID: PMC165471
The Arabidopsis SeedGenes Project
Iris Tzafrir, Allan Dickerman, Olga Brazhnik, Quoc Nguyen, John McElver, Catherine Frye, David Patton, and David Meinke
Nucleic Acids Res. 2003 January 1; 31(1): 90–93.
PMCID: PMC165475
The Stanford Microarray Database: data access and quality assessment tools
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
Nucleic Acids Res. 2003 January 1; 31(1): 94–96.
PMCID: PMC165525
TRANSPATH®: an integrated database on signal transduction and a tool for array analysis
Mathias Krull, Nico Voss, Claudia Choi, Susanne Pistor, Anatolij Potapov, and Edgar Wingender
Nucleic Acids Res. 2003 January 1; 31(1): 97–100.
PMCID: PMC165536
ASAP: the Alternative Splicing Annotation Project
Christopher Lee, Levan Atanelov, Barmak Modrek, and Yi Xing
Nucleic Acids Res. 2003 January 1; 31(1): 101–105.
PMCID: PMC165476
MICdb: database of prokaryotic microsatellites
Vattipally B. Sreenu, Vishwanath Alevoor, Javaregowda Nagaraju, and Hampapathalu A. Nagarajaram
Nucleic Acids Res. 2003 January 1; 31(1): 106–108.
PMCID: PMC165449
PACRAT: a database and analysis system for archaeal and bacterial intergenic sequence features
William C. Ray and Charles J. Daniels
Nucleic Acids Res. 2003 January 1; 31(1): 109–113.
PMCID: PMC165460
PlantProm: a database of plant promoter sequences
Ilham A. Shahmuradov, Alex J. Gammerman, John M. Hancock, Peter M. Bramley, and Victor V. Solovyev
Nucleic Acids Res. 2003 January 1; 31(1): 114–117.
PMCID: PMC165488
rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation
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
Nucleic Acids Res. 2003 January 1; 31(1): 118–121.
PMCID: PMC165559
RTPrimerDB: the Real-Time PCR primer and probe database
Filip Pattyn, Frank Speleman, Anne De Paepe, and Jo Vandesompele
Nucleic Acids Res. 2003 January 1; 31(1): 122–123.
PMCID: PMC165458
The SNP Consortium website: past, present and future
Gudmundur A. Thorisson and Lincoln D. Stein
Nucleic Acids Res. 2003 January 1; 31(1): 124–127.
PMCID: PMC165499
Sputnik: a database platform for comparative plant genomics
Stephen Rudd, Hans-Werner Mewes, and Klaus F.X. Mayer
Nucleic Acids Res. 2003 January 1; 31(1): 128–132.
PMCID: PMC165522
WormBase: a cross-species database for comparative genomics
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
Nucleic Acids Res. 2003 January 1; 31(1): 133–137.
PMCID: PMC165500
The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa)
Emmanuelle Karsenty, Emmanuel Barillot, Gwenola Tosser-Klopp, Yvette Lahbib-Mansais, Denis Milan, François Hatey, Susanna Cirera, Milena Sawera, Claus B. Jørgensen, Bhanu Chowdhary, Merete Fredholm, Klaus Wimmers, Siriluck Ponsuksili, Roberta Davoli, Luca Fontanesi, Silvia Braglia, Paolo Zambonelli, Daniele Bigi, Stefan Neuenschwander, and Joël Gellin
Nucleic Acids Res. 2003 January 1; 31(1): 138–141.
PMCID: PMC165508
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE
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
Nucleic Acids Res. 2003 January 1; 31(1): 142–146.
PMCID: PMC165497
ASAP, a systematic annotation package for community analysis of genomes
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
Nucleic Acids Res. 2003 January 1; 31(1): 147–151.
PMCID: PMC165572
BSD: the Biodegradative Strain Database
John W. Urbance, James Cole, Paul Saxman, and James M. Tiedje
Nucleic Acids Res. 2003 January 1; 31(1): 152–155.
PMCID: PMC165479
CATMA: a complete Arabidopsis GST database
Mark L. Crowe, Carine Serizet, Vincent Thareau, Sébastien Aubourg, Pierre Rouzé, Pierre Hilson, Jim Beynon, Peter Weisbeek, Paul van Hummelen, Philippe Reymond, Javier Paz-Ares, Wilfried Nietfeld, and Martin Trick
Nucleic Acids Res. 2003 January 1; 31(1): 156–158.
PMCID: PMC165518
CnidBase: The Cnidarian Evolutionary Genomics Database
Joseph F. Ryan and John R. Finnerty
Nucleic Acids Res. 2003 January 1; 31(1): 159–163.
PMCID: PMC165563
The ERGOTM genome analysis and discovery system
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
Nucleic Acids Res. 2003 January 1; 31(1): 164–171.
PMCID: PMC165577
The FlyBase database of the Drosophila genome projects and community literature
Nucleic Acids Res. 2003 January 1; 31(1): 172–175.
PMCID: PMC165541
GOBASE—a database of mitochondrial and chloroplast information
Emmet A. O'Brien, Elarbi Badidi, Ania Barbasiewicz, Cristina deSousa, B. Franz Lang, and Gertraud Burger
Nucleic Acids Res. 2003 January 1; 31(1): 176–178.
PMCID: PMC165537
GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics
Delphine Samson, Fabrice Legeai, Emmanuelle Karsenty, Sébastien Reboux, Jean-Baptiste Veyrieras, Jeremy Just, and Emmanuel Barillot
Nucleic Acids Res. 2003 January 1; 31(1): 179–182.
PMCID: PMC165507
GrainGenes, the genome database for small-grain crops
David E. Matthews, Victoria L. Carollo, Gerard R. Lazo, and Olin D. Anderson
Nucleic Acids Res. 2003 January 1; 31(1): 183–186.
PMCID: PMC165505
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes
S. Garcia-Vallve, E. Guzman, M. A. Montero, and A. Romeu
Nucleic Acids Res. 2003 January 1; 31(1): 187–189.
PMCID: PMC165451
MOsDB: an integrated information resource for rice genomics
Wojciech M. Karlowski, Heiko Schoof, Vijayalakshmi Janakiraman, Volker Stuempflen, and Klaus F. X. Mayer
Nucleic Acids Res. 2003 January 1; 31(1): 190–192.
PMCID: PMC165520
MGD: the Mouse Genome Database
Judith A. Blake, Joel E. Richardson, Carol J. Bult, Jim A. Kadin, Janan T. Eppig, and The Mouse Genome Database Group
Nucleic Acids Res. 2003 January 1; 31(1): 193–195.
PMCID: PMC165494
MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome
Anne-Françoise J. Lamblin, John A. Crow, James E. Johnson, Kevin A. T. Silverstein, Timothy M. Kunau, Alan Kilian, Diane Benz, Martina Stromvik, Gabriella Endré, Kathryn A. VandenBosch, Douglas R. Cook, Nevin D. Young, and Ernest F. Retzel
Nucleic Acids Res. 2003 January 1; 31(1): 196–201.
PMCID: PMC165566
OGRe: a relational database for comparative analysis of mitochondrial genomes
Daniel Jameson, Andrew P. Gibson, Cendrine Hudelot, and Paul G. Higgs
Nucleic Acids Res. 2003 January 1; 31(1): 202–206.
PMCID: PMC165524
The PEDANT genome database
Dmitrij Frishman, Martin Mokrejs, Denis Kosykh, Gabi Kastenmüller, Grigory Kolesov, Igor Zubrzycki, Christian Gruber, Birgitta Geier, Andreas Kaps, Kaj Albermann, Andreas Volz, Christian Wagner, Matthias Fellenberg, Klaus Heumann, and Hans-Werner Mewes
Nucleic Acids Res. 2003 January 1; 31(1): 207–211.
PMCID: PMC165452
PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
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
Nucleic Acids Res. 2003 January 1; 31(1): 212–215.
PMCID: PMC165528
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins
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
Nucleic Acids Res. 2003 January 1; 31(1): 216–218.
PMCID: PMC165501
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
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
Nucleic Acids Res. 2003 January 1; 31(1): 219–223.
PMCID: PMC165461
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
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
Nucleic Acids Res. 2003 January 1; 31(1): 224–228.
PMCID: PMC165523
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists
Qiaoping Yuan, Shu Ouyang, Jia Liu, Bernard Suh, Foo Cheung, Razvan Sultana, Dan Lee, John Quackenbush, and C. Robin Buell
Nucleic Acids Res. 2003 January 1; 31(1): 229–233.
PMCID: PMC165506
ToxoDB: accessing the Toxoplasma gondii genome
Jessica C. Kissinger, Bindu Gajria, Li Li, Ian T. Paulsen, and David S. Roos
Nucleic Acids Res. 2003 January 1; 31(1): 234–236.
PMCID: PMC165519
WorfDB: the Caenorhabditis elegans ORFeome Database
Philippe Vaglio, Philippe Lamesch, Jérôme Reboul, Jean-François Rual, Monica Martinez, David Hill, and Marc Vidal
Nucleic Acids Res. 2003 January 1; 31(1): 237–240.
PMCID: PMC165539
The Zebrafish Information Network (ZFIN): the zebrafish model organism database
Judy Sprague, Dave Clements, Tom Conlin, Pat Edwards, Ken Frazer, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, and Monte Westerfield
Nucleic Acids Res. 2003 January 1; 31(1): 241–243.
PMCID: PMC165474
ZmDB, an integrated database for maize genome research
Qunfeng Dong, Laura Roy, Michael Freeling, Virginia Walbot, and Volker Brendel
Nucleic Acids Res. 2003 January 1; 31(1): 244–247.
PMCID: PMC165529
BIND: the Biomolecular Interaction Network Database
Gary D. Bader, Doron Betel, and Christopher W. V. Hogue
Nucleic Acids Res. 2003 January 1; 31(1): 248–250.
PMCID: PMC165503
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes
See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan, and Kui Lin
Nucleic Acids Res. 2003 January 1; 31(1): 251–254.
PMCID: PMC165526
KDBI: Kinetic Data of Bio-molecular Interactions database
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
Nucleic Acids Res. 2003 January 1; 31(1): 255–257.
PMCID: PMC165514
STRING: a database of predicted functional associations between proteins
Christian von Mering, Martijn Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, and Berend Snel
Nucleic Acids Res. 2003 January 1; 31(1): 258–261.
PMCID: PMC165481
The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining
Lynda B. M. Ellis, Bo Kyeng Hou, Wenjun Kang, and Lawrence P. Wackett
Nucleic Acids Res. 2003 January 1; 31(1): 262–265.
PMCID: PMC165495
PRODORIC: prokaryotic database of gene regulation
Richard Münch, Karsten Hiller, Heiko Barg, Dana Heldt, Simone Linz, Edgar Wingender, and Dieter Jahn
Nucleic Acids Res. 2003 January 1; 31(1): 266–269.
PMCID: PMC165484
ALFRED: the ALelle FREquency Database. Update
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
Nucleic Acids Res. 2003 January 1; 31(1): 270–271.
PMCID: PMC165490
Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003
Jean-Loup Huret, Philippe Dessen, and Alain Bernheim
Nucleic Acids Res. 2003 January 1; 31(1): 272–274.
PMCID: PMC165573
Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals
Frank W. Nicholas
Nucleic Acids Res. 2003 January 1; 31(1): 275–277.
PMCID: PMC165521
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells
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
Nucleic Acids Res. 2003 January 1; 31(1): 278–281.
PMCID: PMC165511
INFEVERS: the Registry for FMF and hereditary inflammatory disorders mutations
Cyril Sarrauste de Menthière, Stéphane Terrière, Denis Pugnère, Manuel Ruiz, Jacques Demaille, and Isabelle Touitou
Nucleic Acids Res. 2003 January 1; 31(1): 282–285.
PMCID: PMC165478
The MetaFMF website: a high quality tool for meta-analysis of FMF
Denis Pugnère, Manuel Ruiz, Cyril Sarrauste de Menthière, Benjamin Masdoua, Jacques Demaille, and Isabelle Touitou
Nucleic Acids Res. 2003 January 1; 31(1): 286–290.
PMCID: PMC165544
PGDB: a curated and integrated database of genes related to the prostate
Long-Cheng Li, Hong Zhao, Hiroaki Shiina, Christopher J. Kane, and Rajvir Dahiya
Nucleic Acids Res. 2003 January 1; 31(1): 291–293.
PMCID: PMC165455
GPCRDB information system for G protein-coupled receptors
Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E. Cohen, and Gerrit Vriend
Nucleic Acids Res. 2003 January 1; 31(1): 294–297.
PMCID: PMC165550
Human immunodeficiency virus reverse transcriptase and protease sequence database
Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, and Robert W. Shafer
Nucleic Acids Res. 2003 January 1; 31(1): 298–303.
PMCID: PMC165547
The Homeodomain Resource: 2003 update
Sharmila Banerjee-Basu, Travis Moreland, Benjamin J. Hsu, Kenneth L. Trout, and Andreas D. Baxevanis
Nucleic Acids Res. 2003 January 1; 31(1): 304–306.
PMCID: PMC165565
IMGT, the international ImMunoGeneTics database®
Marie-Paule Lefranc
Nucleic Acids Res. 2003 January 1; 31(1): 307–310.
PMCID: PMC165532
IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex
James Robinson, Matthew J. Waller, Peter Parham, Natasja de Groot, Ronald Bontrop, Lorna J. Kennedy, Peter Stoehr, and Steven G. E. Marsh
Nucleic Acids Res. 2003 January 1; 31(1): 311–314.
PMCID: PMC165517
The InterPro Database, 2003 brings increased coverage and new features
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
Nucleic Acids Res. 2003 January 1; 31(1): 315–318.
PMCID: PMC165493
The Lipase Engineering Database: a navigation and analysis tool for protein families
Markus Fischer and Jürgen Pleiss
Nucleic Acids Res. 2003 January 1; 31(1): 319–321.
PMCID: PMC165462
MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion
Marco Sardiello, Flavio Licciulli, Domenico Catalano, Marcella Attimonelli, and Corrado Caggese
Nucleic Acids Res. 2003 January 1; 31(1): 322–324.
PMCID: PMC165570
The Mitochondrial Protein Import Machinery of Plants (MPIMP) database
Ryan Lister, Monika W. Murcha, and James Whelan
Nucleic Acids Res. 2003 January 1; 31(1): 325–327.
PMCID: PMC165502
The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome
G. Dellaire, R. Farrall, and W.A. Bickmore
Nucleic Acids Res. 2003 January 1; 31(1): 328–330.
PMCID: PMC165465
NRMD: Nuclear Receptor Mutation Database
Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, and Gert Vriend
Nucleic Acids Res. 2003 January 1; 31(1): 331–333.
PMCID: PMC165569
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification
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
Nucleic Acids Res. 2003 January 1; 31(1): 334–341.
PMCID: PMC165562
The PlantsP and PlantsT Functional Genomics Databases
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
Nucleic Acids Res. 2003 January 1; 31(1): 342–344.
PMCID: PMC165472
The Protein Information Resource
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
Nucleic Acids Res. 2003 January 1; 31(1): 345–347.
PMCID: PMC165487
ProtoNet: hierarchical classification of the protein space
Ori Sasson, Avishay Vaaknin, Hillel Fleischer, Elon Portugaly, Yonatan Bilu, Nathan Linial, and Michal Linial
Nucleic Acids Res. 2003 January 1; 31(1): 348–352.
PMCID: PMC165543
RTKdb: database of receptor tyrosine kinase
Julien Grassot, Guy Mouchiroud, and Guy Perrière
Nucleic Acids Res. 2003 January 1; 31(1): 353–358.
PMCID: PMC165483
SDAP: database and computational tools for allergenic proteins
Ovidiu Ivanciuc, Catherine H. Schein, and Werner Braun
Nucleic Acids Res. 2003 January 1; 31(1): 359–362.
PMCID: PMC165457
SRPDB: Signal Recognition Particle Database
Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, and Tore Samuelsson
Nucleic Acids Res. 2003 January 1; 31(1): 363–364.
PMCID: PMC165554
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
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
Nucleic Acids Res. 2003 January 1; 31(1): 365–370.
PMCID: PMC165542
The TIGRFAMs database of protein families
Daniel H. Haft, Jeremy D. Selengut, and Owen White
Nucleic Acids Res. 2003 January 1; 31(1): 371–373.
PMCID: PMC165575
TRANSFAC®: transcriptional regulation, from patterns to profiles
V. Matys, E. Fricke, R. Geffers, E. Gößling, 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. Münch, I. Reuter, S. Rotert, H. Saxel, M. Scheer, S. Thiele, and E. Wingender
Nucleic Acids Res. 2003 January 1; 31(1): 374–378.
PMCID: PMC165555
Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences
Angelo M. Facchiano, Antonio Facchiano, and Francesco Facchiano
Nucleic Acids Res. 2003 January 1; 31(1): 379–382.
PMCID: PMC165489
CDD: a curated Entrez database of conserved domain alignments
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
Nucleic Acids Res. 2003 January 1; 31(1): 383–387.
PMCID: PMC165534
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters
E. V. Kriventseva, F. Servant, and R. Apweiler
Nucleic Acids Res. 2003 January 1; 31(1): 388–389.
PMCID: PMC165482
iProClass: an integrated database of protein family, function and structure information
Hongzhan Huang, Winona C. Barker, Yongxing Chen, and Cathy H. Wu
Nucleic Acids Res. 2003 January 1; 31(1): 390–392.
PMCID: PMC165491
NESbase version 1.0: a database of nuclear export signals
Tanja la Cour, Ramneek Gupta, Kristoffer Rapacki, Karen Skriver, Flemming M. Poulsen, and Søren Brunak
Nucleic Acids Res. 2003 January 1; 31(1): 393–396.
PMCID: PMC165548
NLSdb: database of nuclear localization signals
Rajesh Nair, Phil Carter, and Burkhard Rost
Nucleic Acids Res. 2003 January 1; 31(1): 397–399.
PMCID: PMC165448
PRINTS and its automatic supplement, prePRINTS
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
Nucleic Acids Res. 2003 January 1; 31(1): 400–402.
PMCID: PMC165477
The SBASE domain sequence library, release 10: domain architecture prediction
Kristian Vlahoviček, Laszló Kaján, János Murvai, Zoltán Hegedűs, and Sándor Pongor
Nucleic Acids Res. 2003 January 1; 31(1): 403–405.
PMCID: PMC165545
TMPDB: a database of experimentally-characterized transmembrane topologies
Masami Ikeda, Masafumi Arai, Toshikatsu Okuno, and Toshio Shimizu
Nucleic Acids Res. 2003 January 1; 31(1): 406–409.
PMCID: PMC165467
PEP: Predictions for Entire Proteomes
Phil Carter, Jinfeng Liu, and Burkhard Rost
Nucleic Acids Res. 2003 January 1; 31(1): 410–413.
PMCID: PMC165549
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes
Manuela Pruess, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia Kriventseva, Virginie Mittard, Nicola Mulder, Isabelle Phan, Florence Servant, and Rolf Apweiler
Nucleic Acids Res. 2003 January 1; 31(1): 414–417.
PMCID: PMC165552
REBASE: restriction enzymes and methyltransferases
Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis
Nucleic Acids Res. 2003 January 1; 31(1): 418–420.
PMCID: PMC165516
ARED 2.0: an update of AU-rich element mRNA database
Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar
Nucleic Acids Res. 2003 January 1; 31(1): 421–423.
PMCID: PMC165470
Database for mobile group II introns
Lixin Dai, Navtej Toor, Robert Olson, Andrew Keeping, and Steven Zimmerly
Nucleic Acids Res. 2003 January 1; 31(1): 424–426.
PMCID: PMC165496
IRESdb: the Internal Ribosome Entry Site database
Sophie Bonnal, Christel Boutonnet, Leonel Prado-Lourenço, and Stéphan Vagner
Nucleic Acids Res. 2003 January 1; 31(1): 427–428.
PMCID: PMC165450
Noncoding regulatory RNAs database
Maciej Szymański, Volker A. Erdmann, and Jan Barciszewski
Nucleic Acids Res. 2003 January 1; 31(1): 429–431.
PMCID: PMC165571
Plant snoRNA database
John W. S. Brown, Manuel Echeverria, Liang-Hu Qu, Todd M. Lowe, Jean-Pierre Bachellerie, Alexander Hüttenhofer, James P. Kastenmayer, Pamela J. Green, Paul Shaw, and Dave F. Marshall
Nucleic Acids Res. 2003 January 1; 31(1): 432–435.
PMCID: PMC165456
PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes
Guglielmo Rainaldi, Mariateresa Volpicella, Flavio Licciulli, Sabino Liuni, Raffaele Gallerani, and Luigi R. Ceci
Nucleic Acids Res. 2003 January 1; 31(1): 436–438.
PMCID: PMC165527
Rfam: an RNA family database
Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, and Sean R. Eddy
Nucleic Acids Res. 2003 January 1; 31(1): 439–441.
PMCID: PMC165453
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
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
Nucleic Acids Res. 2003 January 1; 31(1): 442–443.
PMCID: PMC165486
SubViral RNA: a database of the smallest known auto-replicable RNA species
Martin Pelchat, Lynda Rocheleau, Jonathan Perreault, and Jean-Pierre Perreault
Nucleic Acids Res. 2003 January 1; 31(1): 444–445.
PMCID: PMC165473
tmRDB (tmRNA database)
Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, and Jacek Wower
Nucleic Acids Res. 2003 January 1; 31(1): 446–447.
PMCID: PMC165466
CADB: Conformation Angles DataBase of proteins
S. S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi, and K. Sekar
Nucleic Acids Res. 2003 January 1; 31(1): 448–451.
PMCID: PMC165531
The CATH database: an extended protein family resource for structural and functional genomics
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
Nucleic Acids Res. 2003 January 1; 31(1): 452–455.
PMCID: PMC165509
DSMM: a Database of Simulated Molecular Motions
Giacomo Finocchiaro, Ting Wang, Rene Hoffmann, Aitor Gonzalez, and Rebecca C. Wade
Nucleic Acids Res. 2003 January 1; 31(1): 456–457.
PMCID: PMC165560
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database
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
Nucleic Acids Res. 2003 January 1; 31(1): 458–462.
PMCID: PMC165512
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species
Akihiro Yamaguchi, Mitsuo Iwadate, Ei-ichiro Suzuki, Kei Yura, Shigetsugu Kawakita, Hideaki Umeyama, and Mitiko Go
Nucleic Acids Res. 2003 January 1; 31(1): 463–468.
PMCID: PMC165564
Gene3D: structural assignments for the biologist and bioinformaticist alike
Daniel W. A. Buchan, Stuart C. G. Rison, James E. Bray, David Lee, Frances Pearl, Janet M. Thornton, and Christine A. Orengo
Nucleic Acids Res. 2003 January 1; 31(1): 469–473.
PMCID: PMC165498
MMDB: Entrez's 3D-structure database
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
Nucleic Acids Res. 2003 January 1; 31(1): 474–477.
PMCID: PMC165533
MolMovDB: analysis and visualization of conformational change and structural flexibility
Nathaniel Echols, Duncan Milburn, and Mark Gerstein
Nucleic Acids Res. 2003 January 1; 31(1): 478–482.
PMCID: PMC165551
NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0
Wing Lok Abe Kurtz Chiu, Chun Ngai Sze, Nap Tak Ma, Lai Fan Chiu, Chung Wai Leung, and Steve Chik Fun Au-Yeung
Nucleic Acids Res. 2003 January 1; 31(1): 483–485.
PMCID: PMC165561
Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database
V. S. Gowri, Shashi B. Pandit, P. S. Karthik, N. Srinivasan, and S. Balaji
Nucleic Acids Res. 2003 January 1; 31(1): 486–488.
PMCID: PMC165510
The Protein Data Bank and structural genomics
John Westbrook, Zukang Feng, Li Chen, Huanwang Yang, and Helen M. Berman
Nucleic Acids Res. 2003 January 1; 31(1): 489–491.
PMCID: PMC165515
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
Tamotsu Noguchi and Yutaka Akiyama
Nucleic Acids Res. 2003 January 1; 31(1): 492–493.
PMCID: PMC165469
The PSSH database of alignments between protein sequences and tertiary structures
Andrea Schafferhans, Joachim E. W. Meyer, and Seán I. O'Donoghue
Nucleic Acids Res. 2003 January 1; 31(1): 494–498.
PMCID: PMC165557
The RESID Database of Protein Modifications: 2003 developments
John S. Garavelli
Nucleic Acids Res. 2003 January 1; 31(1): 499–501.
PMCID: PMC165485
RNABase: an annotated database of RNA structures
Venkatesh L. Murthy and George D. Rose
Nucleic Acids Res. 2003 January 1; 31(1): 502–504.
PMCID: PMC165459
The Structure Superposition Database
Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, and Patricia C. Babbitt
Nucleic Acids Res. 2003 January 1; 31(1): 505–510.
PMCID: PMC165574
GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update
Catherine A. Cooper, Hiren J. Joshi, Mathew J. Harrison, Marc R. Wilkins, and Nicolle H. Packer
Nucleic Acids Res. 2003 January 1; 31(1): 511–513.
PMCID: PMC165546
probeBase: an online resource for rRNA-targeted oligonucleotide probes
Alexander Loy, Matthias Horn, and Michael Wagner
Nucleic Acids Res. 2003 January 1; 31(1): 514–516.
PMCID: PMC165463
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