Nucleic Acids Research

Editorial:

Editorial
Nucl. Acids Res. 2000 28: 0; doi:10.1093/nar/28.1.0 [Print PDF] [Request Permissions]  

Articles:

Andreas D. Baxevanis

The Molecular Biology Database Collection: an online compilation of relevant database resources
Nucl. Acids Res. 2000 28: 1-7; doi:10.1093/nar/28.1.1 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Claude Discala, Xavier Benigni, Emmanuel Barillot, and Guy Vaysseix

DBcat: a catalog of 500 biological databases
Nucl. Acids Res. 2000 28: 8-9; doi:10.1093/nar/28.1.8 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

David L. Wheeler, Colombe Chappey, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Gregory D. Schuler, Tatiana A. Tatusova, and Barbara A. Rapp

Database resources of the National Center for Biotechnology Information
Nucl. Acids Res. 2000 28: 10-14; doi:10.1093/nar/28.1.10 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Barbara A. Rapp, and David L. Wheeler

GenBank
Nucl. Acids Res. 2000 28: 15-18; doi:10.1093/nar/28.1.15 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Wendy Baker, Alexandra van den Broek, Evelyn Camon, Pascal Hingamp, Peter Sterk, Guenter Stoesser, and Mary Ann Tuli

The EMBL Nucleotide Sequence Database
Nucl. Acids Res. 2000 28: 19-23; doi:10.1093/nar/28.1.19 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Yoshio Tateno, Satoru Miyazaki, Motonori Ota, Hideaki Sugawara, and Takashi Gojobori

DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams
Nucl. Acids Res. 2000 28: 24-26; doi:10.1093/nar/28.1.24 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Minoru Kanehisa and Susumu Goto

KEGG: Kyoto Encyclopedia of Genes and Genomes
Nucl. Acids Res. 2000 28: 27-30; doi:10.1093/nar/28.1.27 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

C. Harger, G. Chen, A. Farmer, W. Huang, J. Inman, D. Kiphart, F. Schilkey, M. P. Skupski, and J. Weller

The Genome Sequence DataBase
Nucl. Acids Res. 2000 28: 31-32; doi:10.1093/nar/28.1.31 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Roman L. Tatusov, Michael Y. Galperin, Darren A. Natale, and Eugene V. Koonin

The COG database: a tool for genome-scale analysis of protein functions and evolution
Nucl. Acids Res. 2000 28: 33-36; doi:10.1093/nar/28.1.33 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

H. W. Mewes, D. Frishman, C. Gruber, B. Geier, D. Haase, A. Kaps, K. Lemcke, G. Mannhaupt, F. Pfeiffer, C. Schüller, S. Stocker, and B. Weil

MIPS: a database for genomes and protein sequences
Nucl. Acids Res. 2000 28: 37-40; doi:10.1093/nar/28.1.37 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Winona C. Barker, John S. Garavelli, Hongzhan Huang, Peter B. McGarvey, Bruce C. Orcutt, Geetha Y. Srinivasarao, Chunlin Xiao, Lai-Su L. Yeh, Robert S. Ledley, Joseph F. Janda, Friedhelm Pfeiffer, Hans-Werner Mewes, Akira Tsugita, and Cathy Wu

The Protein Information Resource (PIR)
Nucl. Acids Res. 2000 28: 41-44; doi:10.1093/nar/28.1.41 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Amos Bairoch and Rolf Apweiler

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
Nucl. Acids Res. 2000 28: 45-48; doi:10.1093/nar/28.1.45 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Golan Yona, Nathan Linial, and Michal Linial

ProtoMap: automatic classification of protein sequences and hierarchy of protein families
Nucl. Acids Res. 2000 28: 49-55; doi:10.1093/nar/28.1.49 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter D. Karp, Monica Riley, Milton Saier, Ian T. Paulsen, Suzanne M. Paley, and Alida Pellegrini-Toole

The EcoCyc and MetaCyc databases
Nucl. Acids Res. 2000 28: 56-59; doi:10.1093/nar/28.1.56 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kenneth E. Rudd

EcoGene: a genome sequence database for Escherichia coli K-12
Nucl. Acids Res. 2000 28: 60-64; doi:10.1093/nar/28.1.60 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Frederick R. Blattner, and Julio Collado-Vides

RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12
Nucl. Acids Res. 2000 28: 65-67; doi:10.1093/nar/28.1.65 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Guy Perrière, Philippe Bessières, and Bernard Labedan

EMGLib: the Enhanced Microbial Genomes Library (update 2000)
Nucl. Acids Res. 2000 28: 68-71; doi:10.1093/nar/28.1.68 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yasukazu Nakamura, Takakazu Kaneko, and Satoshi Tabata

CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000
Nucl. Acids Res. 2000 28: 72; doi:10.1093/nar/28.1.72 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Maria C. Costanzo, Jennifer D. Hogan, Michael E. Cusick, Brian P. Davis, Ann M. Fancher, Peter E. Hodges, Pinar Kondu, Carey Lengieza, Jodi E. Lew-Smith, Carol Lingner, Kevin J. Roberg-Perez, Michael Tillberg, Joan E. Brooks, and James I. Garrels

The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information
Nucl. Acids Res. 2000 28: 73-76; doi:10.1093/nar/28.1.73 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Catherine A. Ball, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Laurie Issel-Tarver, Andrew Kasarskis, Charles R. Scafe, Gavin Sherlock, Gail Binkley, Heng Jin, Mira Kaloper, Sidney D. Orr, Mark Schroeder, Shuai Weng, Yan Zhu, David Botstein, and J. Michael Cherry

Integrating functional genomic information into the Saccharomyces Genome Database
Nucl. Acids Res. 2000 28: 77-80; doi:10.1093/nar/28.1.77 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anuj Kumar, Kei-Hoi Cheung, Petra Ross-Macdonald, Paulo S. R. Coelho, Perry Miller, and Michael Snyder

TRIPLES: a database of gene function in Saccharomyces cerevisiae
Nucl. Acids Res. 2000 28: 81-84; doi:10.1093/nar/28.1.81 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Pascal J. Lopez and Bertrand Séraphin

YIDB: the Yeast Intron DataBase
Nucl. Acids Res. 2000 28: 85-86; doi:10.1093/nar/28.1.85 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mark Waugh, Peter Hraber, Jennifer Weller, Yihe Wu, Guonghong Chen, Jeff Inman, Don Kiphart, and Bruno Sobral

The Phytophthora Genome Initiative Database: informatics and analysis for distributed pathogenomic research
Nucl. Acids Res. 2000 28: 87-90; doi:10.1093/nar/28.1.87 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

W. James Kent and Alan M. Zahler

The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans
Nucl. Acids Res. 2000 28: 91-93; doi:10.1093/nar/28.1.91 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Xiaowu Gai, Shailesh Lal, Liqun Xing, Volker Brendel, and Virginia Walbot

Gene discovery using the maize genome database ZmDB
Nucl. Acids Res. 2000 28: 94-96; doi:10.1093/nar/28.1.94 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Katsumi Sakata, Baltazar A. Antonio, Yoshiyuki Mukai, Hideki Nagasaki, Yasumichi Sakai, Kazuyoshi Makino, and Takuji Sasaki

INE: a rice genome database with an integrated map view
Nucl. Acids Res. 2000 28: 97-101; doi:10.1093/nar/28.1.97 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Curtis J. Palm, Nancy A. Federspiel, and Ronald W. Davis

DAtA: Database of Arabidopsis thaliana Annotation
Nucl. Acids Res. 2000 28: 102-103; doi:10.1093/nar/28.1.102 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jo Dicks, Mary Anderson, Linda Cardle, Sam Cartinhour, Matthew Couchman, Guy Davenport, Jeremy Dickson, Mike Gale, David Marshall, Sean May, Hamish McWilliam, Andrew O’Malia, Helen Ougham, Martin Trick, Sean Walsh, and Robbie Waugh

UK CropNet: a collection of databases and bioinformatics resources for crop plant genomics
Nucl. Acids Res. 2000 28: 104-107; doi:10.1093/nar/28.1.104 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Judith A. Blake, Janan T. Eppig, Joel E. Richardson, Muriel T. Davisson, and the Mouse Genome Database Group

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse
Nucl. Acids Res. 2000 28: 108-111; doi:10.1093/nar/28.1.108 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Carol J. Bult, Debra M. Krupke, John P. Sundberg, and Janan T. Eppig

Mouse Tumor Biology Database (MTB): enhancements and current status
Nucl. Acids Res. 2000 28: 112-114; doi:10.1093/nar/28.1.112 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Martin Ringwald, Janan T. Eppig, James A. Kadin, Joel E. Richardson, and the Gene Expression Database Group

GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements
Nucl. Acids Res. 2000 28: 115-119; doi:10.1093/nar/28.1.115 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

R. Ploger, J. Zhang, D. Bassett, R. Reeves, P. Hieter, M. Boguski, and F. Spencer

XREFdb: cross-referencing the genetics and genes of mammals and model organisms
Nucl. Acids Res. 2000 28: 120-122; doi:10.1093/nar/28.1.120 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ross Overbeek, Niels Larsen, Gordon D. Pusch, Mark D’Souza, Evgeni Selkov Jr, Nikos Kyrpides, Michael Fonstein, Natalia Maltsev, and Evgeni Selkov

WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
Nucl. Acids Res. 2000 28: 123-125; doi:10.1093/nar/28.1.123 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Donna R. Maglott, Kenneth S. Katz, Hugues Sicotte, and Kim D. Pruitt

NCBI’s LocusLink and RefSeq
Nucl. Acids Res. 2000 28: 126-128; doi:10.1093/nar/28.1.126 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shaying Zhao

Human BAC Ends
Nucl. Acids Res. 2000 28: 129-132; doi:10.1093/nar/28.1.129 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Takeshi Kawashima, Shuichi Kawashima, Minoru Kanehisa, Hiroki Nishida, and Kazuhiro W. Makabe

MAGEST: MAboya Gene Expression patterns and Sequence Tags
Nucl. Acids Res. 2000 28: 133-135; doi:10.1093/nar/28.1.133 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Teruyoshi Hishiki, Shoko Kawamoto, Shinichi Morishita, and Kousaku Okubo

BodyMap: a human and mouse gene expression database
Nucl. Acids Res. 2000 28: 136-138; doi:10.1093/nar/28.1.136 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Nicolas Pollet, Heiko A. Schmidt, Volker Gawantka, Martin Vingron, and Christof Niehrs

Axeldb: a Xenopus laevis database focusing on gene expression
Nucl. Acids Res. 2000 28: 139-140; doi:10.1093/nar/28.1.139 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

John Quackenbush, Feng Liang, Ingeborg Holt, Geo Pertea, and Jonathan Upton

The TIGR Gene Indices: reconstruction and representation of expressed gene sequences
Nucl. Acids Res. 2000 28: 141-145; doi:10.1093/nar/28.1.141 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Patricia Rodriguez-Tomé and Philip Lijnzaad

RHdb: the Radiation Hybrid database
Nucl. Acids Res. 2000 28: 146-147; doi:10.1093/nar/28.1.146 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

M. Attimonelli, N. Altamura, R. Benne, A. Brennicke, J. M. Cooper, D. D’Elia, A. de Montalvo, B. de Pinto, M. De Robertis, P. Golik, V. Knoop, C. Lanave, J. Lazowska, F. Licciulli, B. S. Malladi, F. Memeo, M. Monnerot, R. Pasimeni, S. Pilbout, A. H. V. Schapira, P. Sloof, and C. Saccone

MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status
Nucl. Acids Res. 2000 28: 148-152; doi:10.1093/nar/28.1.148 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Cecilia Lanave, Sabino Liuni, Flavio Licciulli, and Marcella Attimonelli

Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences
Nucl. Acids Res. 2000 28: 153-154; doi:10.1093/nar/28.1.153 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

C. Scharfe, P. Zaccaria, K. Hoertnagel, M. Jaksch, T. Klopstock, M. Dembowski, R. Lill, H. Prokisch, K. D. Gerbitz, W. Neupert, H. W. Mewes, and T. Meitinger

MITOP, the mitochondrial proteome database: 2000 update
Nucl. Acids Res. 2000 28: 155-158; doi:10.1093/nar/28.1.155 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Vito Volpetti, Raffaele Gallerani, Caterina De Benedetto, Sabino Liuni, Flavio Licciulli, and Luigi R. Ceci

PLMItRNA, a database for tRNAs and tRNA genes in plant mitochondria: enlargement and updating
Nucl. Acids Res. 2000 28: 159-162; doi:10.1093/nar/28.1.159 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Graziano Pesole, Carmela Gissi, Domenico Catalano, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Marcella Attimonelli, and Cecilia Saccone

MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins
Nucl. Acids Res. 2000 28: 163-165; doi:10.1093/nar/28.1.163 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maciej Szymanski, Miroslawa Z. Barciszewska, Jan Barciszewski, and Volker A. Erdmann

5S ribosomal RNA database Y2K
Nucl. Acids Res. 2000 28: 166-167; doi:10.1093/nar/28.1.166 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kelly P. Williams

The tmRNA Website
Nucl. Acids Res. 2000 28: 168-1; doi:10.1093/nar/28.1.168 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christian Zwieb and Jacek Wower

tmRDB (tmRNA database)
Nucl. Acids Res. 2000 28: 169-170; doi:10.1093/nar/28.1.169 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christian Zwieb and Tore Samuelsson

SRPDB (Signal Recognition Particle Database)
Nucl. Acids Res. 2000 28: 171-172; doi:10.1093/nar/28.1.171 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker, Jr, Paul R. Saxman, Jason M. Stredwick, George M. Garrity, Bing Li, Gary J. Olsen, Sakti Pramanik, Thomas M. Schmidt, and James M. Tiedje

The RDP (Ribosomal Database Project) continues
Nucl. Acids Res. 2000 28: 173-174; doi:10.1093/nar/28.1.173 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yves Van de Peer, Peter De Rijk, Jan Wuyts, Tina Winkelmans, and Rupert De Wachter

The European Small Subunit Ribosomal RNA database
Nucl. Acids Res. 2000 28: 175-176; doi:10.1093/nar/28.1.175 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Peter De Rijk, Jan Wuyts, Yves Van de Peer, Tina Winkelmans, and Rupert De Wachter

The European Large Subunit Ribosomal RNA database
Nucl. Acids Res. 2000 28: 177-178; doi:10.1093/nar/28.1.177 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Martin Pelchat, Patrick Deschênes, and Jean-Pierre Perreault

The database of the smallest known auto-replicable RNA species: viroids and viroid-like RNAs
Nucl. Acids Res. 2000 28: 179-180; doi:10.1093/nar/28.1.179 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nicholas J. Schisler and Jeffrey D. Palmer

The IDB and IEDB: intron sequence and evolution databases
Nucl. Acids Res. 2000 28: 181-184; doi:10.1093/nar/28.1.181 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Serge Saxonov, Iraj Daizadeh, Alexei Fedorov, and Walter Gilbert

EID: the Exon–Intron Database—an exhaustive database of protein-coding intron-containing genes
Nucl. Acids Res. 2000 28: 185-190; doi:10.1093/nar/28.1.185 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

M. Sakharkar, M. Long, T. W. Tan, and S. J. de Souza

ExInt: an Exon/Intron database
Nucl. Acids Res. 2000 28: 191-192; doi:10.1093/nar/28.1.191 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Graziano Pesole, Sabino Liuni, Giorgio Grillo, Flavio Licciulli, Alessandra Larizza, Wojciech Makalowski, and Cecilia Saccone

UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs
Nucl. Acids Res. 2000 28: 193-196; doi:10.1093/nar/28.1.193 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Volker A. Erdmann, Maciej Szymanski, Abraham Hochberg, Nathan de Groot, and Jan Barciszewski

Non-coding, mRNA-like RNAs database Y2K
Nucl. Acids Res. 2000 28: 197-200; doi:10.1093/nar/28.1.197 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

F. H. D. van Batenburg, A. P. Gultyaev, C. W. A. Pleij, J. Ng, and J. Oliehoek

PseudoBase: a database with RNA pseudoknots
Nucl. Acids Res. 2000 28: 201-204; doi:10.1093/nar/28.1.201 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Julia V. Ponomarenko, Galina V. Orlova, Mikhail P. Ponomarenko, Sergey V. Lavryushev, Anatoly S. Frolov, Svetlana V. Zybova, and Nikolay A. Kolchanov

SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation
Nucl. Acids Res. 2000 28: 205-208; doi:10.1093/nar/28.1.205 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

John S. Garavelli

The RESID Database of protein structure modifications: 2000 update
Nucl. Acids Res. 2000 28: 209-211; doi:10.1093/nar/28.1.209 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter S. Nelson, Nigel Clegg, Burak Eroglu, Victoria Hawkins, Roger Bumgarner, Todd Smith, and Leroy Hood

The Prostate Expression Database (PEDB): status and enhancements in 2000
Nucl. Acids Res. 2000 28: 212-213; doi:10.1093/nar/28.1.212 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

George Johnson and Tai Te Wu

Kabat Database and its applications: 30 years after the first variability plot
Nucl. Acids Res. 2000 28: 214-218; doi:10.1093/nar/28.1.214 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Manuel Ruiz, Véronique Giudicelli, Chantal Ginestoux, Peter Stoehr, James Robinson, Julia Bodmer, Steven G. E. Marsh, Ronald Bontrop, Marc Lemaitre, Gérard Lefranc, Denys Chaume, and Marie-Paule Lefranc

IMGT, the international ImMunoGeneTics database
Nucl. Acids Res. 2000 28: 219-221; doi:10.1093/nar/28.1.219 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christian Schönbach, Judice L.Y. Koh, Xin Sheng, Limsoon Wong, and Vladimir Brusic

FIMM, a database of functional molecular immunology
Nucl. Acids Res. 2000 28: 222-224; doi:10.1093/nar/28.1.222 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

T. K. Attwood, M. D. R. Croning, D. R. Flower, A. P. Lewis, J. E. Mabey, P. Scordis, J. N. Selley, and W. Wright

PRINTS-S: the database formerly known as PRINTS
Nucl. Acids Res. 2000 28: 225-227; doi:10.1093/nar/28.1.225 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Jorja G. Henikoff, Elizabeth A. Greene, Shmuel Pietrokovski, and Steven Henikoff

Increased coverage of protein families with the Blocks Database servers
Nucl. Acids Res. 2000 28: 228-230; doi:10.1093/nar/28.1.228 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jörg Schultz, Richard R. Copley, Tobias Doerks, Chris P. Ponting, and Peer Bork

SMART: a web-based tool for the study of genetically mobile domains
Nucl. Acids Res. 2000 28: 231-234; doi:10.1093/nar/28.1.231 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Helen M. Berman, John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, and Philip E. Bourne

The Protein Data Bank
Nucl. Acids Res. 2000 28: 235-242; doi:10.1093/nar/28.1.235 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yanli Wang, Kenneth J. Addess, Lewis Geer, Thomas Madej, Aron Marchler-Bauer, Diane Zimmerman, and Stephen H. Bryant

MMDB: 3D structure data in Entrez
Nucl. Acids Res. 2000 28: 243-245; doi:10.1093/nar/28.1.243 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jan Reichert, Andreas Jabs, Peter Slickers, and Jürgen Sühnel

The IMB Jena Image Library of Biological Macromolecules
Nucl. Acids Res. 2000 28: 246-249; doi:10.1093/nar/28.1.246 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Roberto Sánchez, Ursula Pieper, Neboja Mirkovi, Paul I. W. de Bakker, Edward Wittenstein, and Andrej ali

MODBASE, a database of annotated comparative protein structure models
Nucl. Acids Res. 2000 28: 250-253; doi:10.1093/nar/28.1.250 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Steven E. Brenner, Patrice Koehl, and Michael Levitt

The ASTRAL compendium for protein structure and sequence analysis
Nucl. Acids Res. 2000 28: 254-256; doi:10.1093/nar/28.1.254 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Loredana Lo Conte, Bart Ailey, Tim J. P. Hubbard, Steven E. Brenner, Alexey G. Murzin, and Cyrus Chothia

SCOP: a Structural Classification of Proteins database
Nucl. Acids Res. 2000 28: 257-259; doi:10.1093/nar/28.1.257 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

János Murvai, Kristian Vlahovicek, Endre Barta, Bruno Cataletto, and Sándor Pongor

The SBASE protein domain library, release 7.0: a collection of annotated protein sequence segments
Nucl. Acids Res. 2000 28: 260-262; doi:10.1093/nar/28.1.260 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alex Bateman, Ewan Birney, Richard Durbin, Sean R. Eddy, Kevin L. Howe, and Erik L. L. Sonnhammer

The Pfam Protein Families Database
Nucl. Acids Res. 2000 28: 263-266; doi:10.1093/nar/28.1.263 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Florence Corpet, Florence Servant, Jérôme Gouzy, and Daniel Kahn

ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons
Nucl. Acids Res. 2000 28: 267-269; doi:10.1093/nar/28.1.267 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

A. Krause, J. Stoye, and M. Vingron

The SYSTERS protein sequence cluster set
Nucl. Acids Res. 2000 28: 270-272; doi:10.1093/nar/28.1.270 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hongzhan Huang, Chunlin Xiao, and Cathy H. Wu

ProClass protein family database
Nucl. Acids Res. 2000 28: 273-276; doi:10.1093/nar/28.1.273 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Frances M. G. Pearl, David Lee, James E. Bray, Ian Sillitoe, Annabel E. Todd, Andrew P. Harrison, Janet M. Thornton, and Christine A. Orengo

Assigning genomic sequences to CATH
Nucl. Acids Res. 2000 28: 277-282; doi:10.1093/nar/28.1.277 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

M. Michael Gromiha, Jianghong An, Hidetoshi Kono, Motohisa Oobatake, Hatsuho Uedaira, P. Prabakaran, and Akinori Sarai

ProTherm, version 2.0: thermodynamic database for proteins and mutants
Nucl. Acids Res. 2000 28: 283-285; doi:10.1093/nar/28.1.283 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Christine Hoogland, Jean-Charles Sanchez, Luisa Tonella, Pierre-Alain Binz, Amos Bairoch, Denis F. Hochstrasser, and Ron D. Appel

The 1999 SWISS-2DPAGE database update
Nucl. Acids Res. 2000 28: 286-288; doi:10.1093/nar/28.1.286 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ioannis Xenarios, Danny W. Rice, Lukasz Salwinski, Marisa K. Baron, Edward M. Marcotte, and David Eisenberg

DIP: the Database of Interacting Proteins
Nucl. Acids Res. 2000 28: 289-291; doi:10.1093/nar/28.1.289 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yasukazu Nakamura, Takashi Gojobori, and Toshimichi Ikemura

Codon usage tabulated from international DNA sequence databases: status for the year 2000
Nucl. Acids Res. 2000 28: 292; doi:10.1093/nar/28.1.292 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Grant H. Jacobs, Peter A. Stockwell, Mark J. Schrieber, Warren P. Tate, and Chris M. Brown

Transterm: a database of messenger RNA components and signals
Nucl. Acids Res. 2000 28: 293-295; doi:10.1093/nar/28.1.293 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

I. Dralyuk, M. Brudno, M. S. Gelfand, M. Zorn, and I. Dubchak

ASDB: database of alternatively spliced genes
Nucl. Acids Res. 2000 28: 296-297; doi:10.1093/nar/28.1.296 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

N. A. Kolchanov, O. A. Podkolodnaya, E. A. Ananko, E. V. Ignatieva, I. L. Stepanenko, O. V. Kel-Margoulis, A. E. Kel, T. I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, F. A. Kolpakov, N. L. Podkolodny, A. N. Naumochkin, I. M. Korostishevskaya, A. G. Romashchenko, and G. C. Overton

Transcription Regulatory Regions Database (TRRD): its status in 2000
Nucl. Acids Res. 2000 28: 298-301; doi:10.1093/nar/28.1.298 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rouaïda Cavin Périer, Viviane Praz, Thomas Junier, Claude Bonnard, and Philipp Bucher

The Eukaryotic Promoter Database (EPD)
Nucl. Acids Res. 2000 28: 302-303; doi:10.1093/nar/28.1.302 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Amos Bairoch

The ENZYME database in 2000
Nucl. Acids Res. 2000 28: 304-305; doi:10.1093/nar/28.1.304 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Richard J. Roberts and Dana Macelis

REBASE – restriction enzymes and methylases
Nucl. Acids Res. 2000 28: 306-307; doi:10.1093/nar/28.1.306 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

David Ghosh

Object-oriented Transcription Factors Database (ooTFD)
Nucl. Acids Res. 2000 28: 308-310; doi:10.1093/nar/28.1.308 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Olga V. Kel-Margoulis, Aida G. Romashchenko, Nikolay A. Kolchanov, Edgar Wingender, and Alexander E. Kel

COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation
Nucl. Acids Res. 2000 28: 311-315; doi:10.1093/nar/28.1.311 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

E. Wingender, X. Chen, R. Hehl, H. Karas, I. Liebich, V. Matys, T. Meinhardt, M. Prüß, I. Reuter, and F. Schacherer

TRANSFAC: an integrated system for gene expression regulation
Nucl. Acids Res. 2000 28: 316-319; doi:10.1093/nar/28.1.316 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Steven A. Sullivan, L. Aravind, Izabela Makalowska, Andreas D. Baxevanis, and David Landsman

The Histone Database: a comprehensive WWW resource for histones and histone fold-containing proteins
Nucl. Acids Res. 2000 28: 320-322; doi:10.1093/nar/28.1.320 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Neil D. Rawlings and Alan J. Barrett

MEROPS: the peptidase database
Nucl. Acids Res. 2000 28: 323-325; doi:10.1093/nar/28.1.323 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Maciej Szymanski and Jan Barciszewski

Aminoacyl-tRNA synthetases database Y2K
Nucl. Acids Res. 2000 28: 326-328; doi:10.1093/nar/28.1.326 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sharmila Banerjee-Basu, Joseph F. Ryan, and Andreas D. Baxevanis

The Homeodomain Resource: a prototype database for a large protein family
Nucl. Acids Res. 2000 28: 329-330; doi:10.1093/nar/28.1.329 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Reiko Kikuno, Takahiro Nagase, Mikita Suyama, Mina Waki, Makoto Hirosawa, and Osamu Ohara

HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project
Nucl. Acids Res. 2000 28: 331-332; doi:10.1093/nar/28.1.331 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Eckhard Jankowsky and Anja Jankowsky

The DExH/D protein family database
Nucl. Acids Res. 2000 28: 333-334; doi:10.1093/nar/28.1.333 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Mark D’Souza, Margaret F. Romine, and Natalia Maltsev

SENTRA, a database of signal transduction proteins
Nucl. Acids Res. 2000 28: 335-336; doi:10.1093/nar/28.1.335 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alexander V. Spirov, Timothy Bowler, and John Reinitz

HOX Pro: a specialized database for clusters and networks of homeobox genes
Nucl. Acids Res. 2000 28: 337-340; doi:10.1093/nar/28.1.337 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Emmanouil Skoufos, Luis Marenco, Prakash M. Nadkarni, Perry L. Miller, and Gordon M. Shepherd

Olfactory Receptor Database: a sensory chemoreceptor resource
Nucl. Acids Res. 2000 28: 341-343; doi:10.1093/nar/28.1.341 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Francine B. Perler

InBase, the Intein Database
Nucl. Acids Res. 2000 28: 344-345; doi:10.1093/nar/28.1.344 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Robert W. Shafer, Duane R. Jung, Bradley J. Betts, Yinong Xi, and Matthew J. Gonzales

Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database
Nucl. Acids Res. 2000 28: 346-348; doi:10.1093/nar/28.1.346 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jean-Loup Huret, Sylvaine Le Minor, Franck Dorkeld, Philippe Dessen, and Alain Bernheim

Atlas of Genetics and Cytogenetics in Oncology and Haematology, an Interactive Database
Nucl. Acids Res. 2000 28: 349-351; doi:10.1093/nar/28.1.349 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Elizabeth M. Smigielski, Karl Sirotkin, Minghong Ward, and Stephen T. Sherry

dbSNP: a database of single nucleotide polymorphisms
Nucl. Acids Res. 2000 28: 352-355; doi:10.1093/nar/28.1.352 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anthony J. Brookes, Heikki Lehväslaiho, Marianne Siegfried, Jana G. Boehm, Yan P. Yuan, Chandra M. Sarkar, Peer Bork, and Flavio Ortigao

HGBASE: a dat