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Other Issues:
 Contents: Volume 31, Number 1  January 1 2003   [Index by Author] 
       Editorial
       Articles
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Editorial:

Editorial
Nucl. Acids. Res. 2003 31: 0. [Full Text]  

Articles:

Andreas D. Baxevanis
The Molecular Biology Database Collection: 2003 update
Nucl. Acids. Res. 2003 31: 1-12. [Abstract] [Full Text] Database Listing  

S. Miyazaki, H. Sugawara, T. Gojobori, and Y. Tateno
DNA Data Bank of Japan (DDBJ) in XML
Nucl. Acids. Res. 2003 31: 13-16. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 17-22. [Abstract] [Full Text]  

Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
GenBank
Nucl. Acids. Res. 2003 31: 23-27. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 28-33. [Abstract] [Full Text]  

Kim D. Pruitt, Tatiana Tatusova, and Donna R. Maglott
NCBI Reference Sequence Project: update and current status
Nucl. Acids. Res. 2003 31: 34-37. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 38-42. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 43-50. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 51-54. [Abstract] [Full Text]  

C. Dieterich, H. Wang, K. Rateitschak, H. Luz, and M. Vingron
CORG: a database for COmparative Regulatory Genomics
Nucl. Acids. Res. 2003 31: 55-57. [Abstract] [Full Text]  

Ikuo Uchiyama
MBGD: microbial genome database for comparative analysis
Nucl. Acids. Res. 2003 31: 58-62. [Abstract] [Full Text]  

Magalie Leveugle, Karine Prat, Nadine Perrier, Daniel Birnbaum, and François Coulier
ParaDB: a tool for paralogy mapping in vertebrate genomes
Nucl. Acids. Res. 2003 31: 63-67. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 68-71. [Abstract] [Full Text]  

Thorsten Henrich, Mirana Ramialison, Rebecca Quiring, Beate Wittbrodt, Makoto Furutani-Seiki, Joachim Wittbrodt, and Hisato Kondoh
MEPD: a Medaka gene expression pattern database
Nucl. Acids. Res. 2003 31: 72-74. [Abstract] [Full Text]  

Céline Amoreira, Winfried Hindermann, and Christoph Grunau
An improved version of the DNA methylation database (MethDB)
Nucl. Acids. Res. 2003 31: 75-77. [Abstract] [Full Text]  

Kevin Roberg-Perez, Corey M. Carlson, and David A. Largaespada
MTID: a database of Sleeping Beauty transposon insertions in mice
Nucl. Acids. Res. 2003 31: 78-81. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 82-86. [Abstract] [Full Text]  

Pavel V. Baranov, Olga L. Gurvich, Andrew W. Hammer, Raymond F. Gesteland, and John F. Atkins
RECODE 2003
Nucl. Acids. Res. 2003 31: 87-89. [Abstract] [Full Text]  

Iris Tzafrir, Allan Dickerman, Olga Brazhnik, Quoc Nguyen, John McElver, Catherine Frye, David Patton, and David Meinke
The Arabidopsis SeedGenes Project
Nucl. Acids. Res. 2003 31: 90-93. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 94-96. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 97-100. [Abstract] [Full Text]  

Christopher Lee, Levan Atanelov, Barmak Modrek, and Yi Xing
ASAP: the Alternative Splicing Annotation Project
Nucl. Acids. Res. 2003 31: 101-105. [Abstract] [Full Text]  

Vattipally B. Sreenu, Vishwanath Alevoor, Javaregowda Nagaraju, and Hampapathalu A. Nagarajaram
MICdb: database of prokaryotic microsatellites
Nucl. Acids. Res. 2003 31: 106-108. [Abstract] [Full Text]  

William C. Ray and Charles J. Daniels
PACRAT: a database and analysis system for archaeal and bacterial intergenic sequence features
Nucl. Acids. Res. 2003 31: 109-113. [Abstract] [Full Text]  

Ilham A. Shahmuradov, Alex J. Gammerman, John M. Hancock, Peter M. Bramley, and Victor V. Solovyev
PlantProm: a database of plant promoter sequences
Nucl. Acids. Res. 2003 31: 114-117. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 118-121. [Abstract] [Full Text]  

Filip Pattyn, Frank Speleman, Anne De Paepe, and Jo Vandesompele
RTPrimerDB: the Real-Time PCR primer and probe database
Nucl. Acids. Res. 2003 31: 122-123. [Abstract] [Full Text]  

Gudmundur A. Thorisson and Lincoln D. Stein
The SNP Consortium website: past, present and future
Nucl. Acids. Res. 2003 31: 124-127. [Abstract] [Full Text]  

Stephen Rudd, Hans-Werner Mewes, and Klaus F.X. Mayer
Sputnik: a database platform for comparative plant genomics
Nucl. Acids. Res. 2003 31: 128-132. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 133-137. [Abstract] [Full Text]  

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
The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa)
Nucl. Acids. Res. 2003 31: 138-141. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 142-146. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 147-151. [Abstract] [Full Text]  

John W. Urbance, James Cole, Paul Saxman, and James M. Tiedje
BSD: the Biodegradative Strain Database
Nucl. Acids. Res. 2003 31: 152-155. [Abstract] [Full Text]  

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
CATMA: a complete Arabidopsis GST database
Nucl. Acids. Res. 2003 31: 156-158. [Abstract] [Full Text]  

Joseph F. Ryan and John R. Finnerty
CnidBase: The Cnidarian Evolutionary Genomics Database
Nucl. Acids. Res. 2003 31: 159-163. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 164-171. [Abstract] [Full Text] Supplementary Material  

The FlyBase database of the Drosophila genome projects and community literature
Nucl. Acids. Res. 2003 31: 172-175. [Abstract] [Full Text]  

Emmet A. O'Brien, Elarbi Badidi, Ania Barbasiewicz, Cristina deSousa, B. Franz Lang, and Gertraud Burger
GOBASE—a database of mitochondrial and chloroplast information
Nucl. Acids. Res. 2003 31: 176-178. [Abstract] [Full Text]  

Delphine Samson, Fabrice Legeai, Emmanuelle Karsenty, Sébastien Reboux, Jean-Baptiste Veyrieras, Jeremy Just, and Emmanuel Barillot
GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics
Nucl. Acids. Res. 2003 31: 179-182. [Abstract] [Full Text]  

David E. Matthews, Victoria L. Carollo, Gerard R. Lazo, and Olin D. Anderson
GrainGenes, the genome database for small-grain crops
Nucl. Acids. Res. 2003 31: 183-186. [Abstract] [Full Text] Supplementary Material  

S. Garcia-Vallve, E. Guzman, M. A. Montero, and A. Romeu
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes
Nucl. Acids. Res. 2003 31: 187-189. [Abstract] [Full Text]  

Wojciech M. Karlowski, Heiko Schoof, Vijayalakshmi Janakiraman, Volker Stuempflen, and Klaus F. X. Mayer
MOsDB: an integrated information resource for rice genomics
Nucl. Acids. Res. 2003 31: 190-192. [Abstract] [Full Text]  

Judith A. Blake, Joel E. Richardson, Carol J. Bult, Jim A. Kadin, and Janan T. Eppig
MGD: the Mouse Genome Database
Nucl. Acids. Res. 2003 31: 193-195. [Abstract] [Full Text] Supplementary Material  

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
MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome
Nucl. Acids. Res. 2003 31: 196-201. [Abstract] [Full Text]  

Daniel Jameson, Andrew P. Gibson, Cendrine Hudelot, and Paul G. Higgs
OGRe: a relational database for comparative analysis of mitochondrial genomes
Nucl. Acids. Res. 2003 31: 202-206. [Abstract] [Full Text]  

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
The PEDANT genome database
Nucl. Acids. Res. 2003 31: 207-211. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 212-215. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 216-218. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 219-223. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 224-228. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 229-233. [Abstract] [Full Text]  

Jessica C. Kissinger, Bindu Gajria, Li Li, Ian T. Paulsen, and David S. Roos
ToxoDB: accessing the Toxoplasma gondii genome
Nucl. Acids. Res. 2003 31: 234-236. [Abstract] [Full Text]  

Philippe Vaglio, Philippe Lamesch, Jérôme Reboul, Jean-François Rual, Monica Martinez, David Hill, and Marc Vidal
WorfDB: the Caenorhabditis elegans ORFeome Database
Nucl. Acids. Res. 2003 31: 237-240. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 241-243. [Abstract] [Full Text]  

Qunfeng Dong, Laura Roy, Michael Freeling, Virginia Walbot, and Volker Brendel
ZmDB, an integrated database for maize genome research
Nucl. Acids. Res. 2003 31: 244-247. [Abstract] [Full Text]  

Gary D. Bader, Doron Betel, and Christopher W. V. Hogue
BIND: the Biomolecular Interaction Network Database
Nucl. Acids. Res. 2003 31: 248-250. [Abstract] [Full Text] Supplementary Material  

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
Nucl. Acids. Res. 2003 31: 251-254. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 255-257. [Abstract] [Full Text]  

Christian von Mering, Martijn Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, and Berend Snel
STRING: a database of predicted functional associations between proteins
Nucl. Acids. Res. 2003 31: 258-261. [Abstract] [Full Text]  

Lynda B. M. Ellis, Bo Kyeng Hou, Wenjun Kang, and Lawrence P. Wackett
The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining
Nucl. Acids. Res. 2003 31: 262-265. [Abstract] [Full Text]  

Richard Münch, Karsten Hiller, Heiko Barg, Dana Heldt, Simone Linz, Edgar Wingender, and Dieter Jahn
PRODORIC: prokaryotic database of gene regulation
Nucl. Acids. Res. 2003 31: 266-269. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 270-271. [Abstract] [Full Text]  

Jean-Loup Huret, Philippe Dessen, and Alain Bernheim
Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003
Nucl. Acids. Res. 2003 31: 272-274. [Abstract] [Full Text]  

Frank W. Nicholas
Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals
Nucl. Acids. Res. 2003 31: 275-277. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 278-281. [Abstract] [Full Text]  

Cyril Sarrauste de Menthière, Stéphane Terrière, Denis Pugnère, Manuel Ruiz, Jacques Demaille, and Isabelle Touitou
INFEVERS: the Registry for FMF and hereditary inflammatory disorders mutations
Nucl. Acids. Res. 2003 31: 282-285. [Abstract] [Full Text]  

Denis Pugnère, Manuel Ruiz, Cyril Sarrauste de Menthière, Benjamin Masdoua, Jacques Demaille, and Isabelle Touitou
The MetaFMF website: a high quality tool for meta-analysis of FMF
Nucl. Acids. Res. 2003 31: 286-290. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 291-293. [Abstract] [Full Text]  

Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E. Cohen, and Gerrit Vriend
GPCRDB information system for G protein-coupled receptors
Nucl. Acids. Res. 2003 31: 294-297. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 298-303. [Abstract] [Full Text]  

Sharmila Banerjee-Basu, Travis Moreland, Benjamin J. Hsu, Kenneth L. Trout, and Andreas D. Baxevanis
The Homeodomain Resource: 2003 update
Nucl. Acids. Res. 2003 31: 304-306. [Abstract] [Full Text]  

Marie-Paule Lefranc
IMGT, the international ImMunoGeneTics database®
Nucl. Acids. Res. 2003 31: 307-310. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 311-314. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 315-318. [Abstract] [Full Text] Supplementary Material  

Markus Fischer and Jürgen Pleiss
The Lipase Engineering Database: a navigation and analysis tool for protein families
Nucl. Acids. Res. 2003 31: 319-321. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 322-324. [Abstract] [Full Text]  

Ryan Lister, Monika W. Murcha, and James Whelan
The Mitochondrial Protein Import Machinery of Plants (MPIMP) database
Nucl. Acids. Res. 2003 31: 325-327. [Abstract] [Full Text]  

G. Dellaire, R. Farrall, and W.A. Bickmore
The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome
Nucl. Acids. Res. 2003 31: 328-330. [Abstract] [Full Text]  

Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, and Gert Vriend
NRMD: Nuclear Receptor Mutation Database
Nucl. Acids. Res. 2003 31: 331-333. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 334-341. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 342-344. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 345-347. [Abstract] [Full Text]  

Ori Sasson, Avishay Vaaknin, Hillel Fleischer, Elon Portugaly, Yonatan Bilu, Nathan Linial, and Michal Linial
ProtoNet: hierarchical classification of the protein space
Nucl. Acids. Res. 2003 31: 348-352. [Abstract] [Full Text]  

Julien Grassot, Guy Mouchiroud, and Guy Perrière
RTKdb: database of receptor tyrosine kinase
Nucl. Acids. Res. 2003 31: 353-358. [Abstract] [Full Text]  

Ovidiu Ivanciuc, Catherine H. Schein, and Werner Braun
SDAP: database and computational tools for allergenic proteins
Nucl. Acids. Res. 2003 31: 359-362. [Abstract] [Full Text]  

Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, and Tore Samuelsson
SRPDB: Signal Recognition Particle Database
Nucl. Acids. Res. 2003 31: 363-364. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 365-370. [Abstract] [Full Text]  

Daniel H. Haft, Jeremy D. Selengut, and Owen White
The TIGRFAMs database of protein families
Nucl. Acids. Res. 2003 31: 371-373. [Abstract] [Full Text]  

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
TRANSFAC®: transcriptional regulation, from patterns to profiles
Nucl. Acids. Res. 2003 31: 374-378. [Abstract] [Full Text]  

Angelo M. Facchiano, Antonio Facchiano, and Francesco Facchiano
Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences
Nucl. Acids. Res. 2003 31: 379-382. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 383-387. [Abstract] [Full Text]  

E. V. Kriventseva, F. Servant, and R. Apweiler
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters
Nucl. Acids. Res. 2003 31: 388-389. [Abstract] [Full Text]  

Hongzhan Huang, Winona C. Barker, Yongxing Chen, and Cathy H. Wu
iProClass: an integrated database of protein family, function and structure information
Nucl. Acids. Res. 2003 31: 390-392. [Abstract] [Full Text]  

Tanja la Cour, Ramneek Gupta, Kristoffer Rapacki, Karen Skriver, Flemming M. Poulsen, and Søren Brunak
NESbase version 1.0: a database of nuclear export signals
Nucl. Acids. Res. 2003 31: 393-396. [Abstract] [Full Text]  

Rajesh Nair, Phil Carter, and Burkhard Rost
NLSdb: database of nuclear localization signals
Nucl. Acids. Res. 2003 31: 397-399. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 400-402. [Abstract] [Full Text]  

Kristian Vlahovicek, Laszló Kaján, János Murvai, Zoltán Hegeds, and Sándor Pongor
The SBASE domain sequence library, release 10: domain architecture prediction
Nucl. Acids. Res. 2003 31: 403-405. [Abstract] [Full Text]  

Masami Ikeda, Masafumi Arai, Toshikatsu Okuno, and Toshio Shimizu
TMPDB: a database of experimentally-characterized transmembrane topologies
Nucl. Acids. Res. 2003 31: 406-409. [Abstract] [Full Text]  

Phil Carter, Jinfeng Liu, and Burkhard Rost
PEP: Predictions for Entire Proteomes
Nucl. Acids. Res. 2003 31: 410-413. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 414-417. [Abstract] [Full Text]  

Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis
REBASE: restriction enzymes and methyltransferases
Nucl. Acids. Res. 2003 31: 418-420. [Abstract] [Full Text]  

Tala Bakheet, Bryan R. G. Williams, and Khalid S. A. Khabar
ARED 2.0: an update of AU-rich element mRNA database
Nucl. Acids. Res. 2003 31: 421-423. [Abstract] [Full Text]  

Lixin Dai, Navtej Toor, Robert Olson, Andrew Keeping, and Steven Zimmerly
Database for mobile group II introns
Nucl. Acids. Res. 2003 31: 424-426. [Abstract] [Full Text]  

Sophie Bonnal, Christel Boutonnet, Leonel Prado-Lourenço, and Stéphan Vagner
IRESdb: the Internal Ribosome Entry Site database
Nucl. Acids. Res. 2003 31: 427-428. [Abstract] [Full Text]  

Maciej Szymanski, Volker A. Erdmann, and Jan Barciszewski
Noncoding regulatory RNAs database
Nucl. Acids. Res. 2003 31: 429-431. [Abstract] [Full Text]  

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
Plant snoRNA database
Nucl. Acids. Res. 2003 31: 432-435. [Abstract] [Full Text] Supplementary Material  

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
Nucl. Acids. Res. 2003 31: 436-438. [Abstract] [Full Text] Supplementary Material  

Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, and Sean R. Eddy
Rfam: an RNA family database
Nucl. Acids. Res. 2003 31: 439-441. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 442-443. [Abstract] [Full Text]  

Martin Pelchat, Lynda Rocheleau, Jonathan Perreault, and Jean-Pierre Perreault
SubViral RNA: a database of the smallest known auto-replicable RNA species
Nucl. Acids. Res. 2003 31: 444-445. [Abstract] [Full Text]  

Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, and Jacek Wower
tmRDB (tmRNA database)
Nucl. Acids. Res. 2003 31: 446-447. [Abstract] [Full Text]  

S. S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi, and K. Sekar
CADB: Conformation Angles DataBase of proteins
Nucl. Acids. Res. 2003 31: 448-451. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 452-455. [Abstract] [Full Text]  

Giacomo Finocchiaro, Ting Wang, Rene Hoffmann, Aitor Gonzalez, and Rebecca C. Wade
DSMM: a Database of Simulated Molecular Motions
Nucl. Acids. Res. 2003 31: 456-457. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 458-462. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 463-468. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 469-473. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 474-477. [Abstract] [Full Text]  

Nathaniel Echols, Duncan Milburn, and Mark Gerstein
MolMovDB: analysis and visualization of conformational change and structural flexibility
Nucl. Acids. Res. 2003 31: 478-482. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 483-485. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 486-488. [Abstract] [Full Text]  

John Westbrook, Zukang Feng, Li Chen, Huanwang Yang, and Helen M. Berman
The Protein Data Bank and structural genomics
Nucl. Acids. Res. 2003 31: 489-491. [Abstract] [Full Text]  

Tamotsu Noguchi and Yutaka Akiyama
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
Nucl. Acids. Res. 2003 31: 492-493. [Abstract] [Full Text]  

Andrea Schafferhans, Joachim E. W. Meyer, and Seán I. O'Donoghue
The PSSH database of alignments between protein sequences and tertiary structures
Nucl. Acids. Res. 2003 31: 494-498. [Abstract] [Full Text]  

John S. Garavelli
The RESID Database of Protein Modifications: 2003 developments
Nucl. Acids. Res. 2003 31: 499-501. [Abstract] [Full Text]  

Venkatesh L. Murthy and George D. Rose
RNABase: an annotated database of RNA structures
Nucl. Acids. Res. 2003 31: 502-504. [Abstract] [Full Text]  

Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, and Patricia C. Babbitt
The Structure Superposition Database
Nucl. Acids. Res. 2003 31: 505-510. [Abstract] [Full Text]  

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
Nucl. Acids. Res. 2003 31: 511-513. [Abstract] [Full Text]  

Alexander Loy, Matthias Horn, and Michael Wagner
probeBase: an online resource for rRNA-targeted oligonucleotide probes
Nucl. Acids. Res. 2003 31: 514-516. [Abstract] [Full Text]  

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