Nucl. Acids Res. -- Table of Contents (29 [1, January 1 2001])

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Contents: Volume 29, Number 1    January 1 2001    [Index by Author]

       Editorial

       Articles

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Editorial:

: Editorial
Nucl. Acids Res. 2001 29: 0; doi:10.1093/nar/29.1.0 [Print PDF] [Request Permissions]

Articles:

Andreas D. Baxevanis: The Molecular Biology Database Collection: an updated compilation of biological database resources
Nucl. Acids Res. 2001 29: 1-10; doi:10.1093/nar/29.1.1 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

David L. Wheeler, Deanna M. Church, Alex E. Lash, Detlef D. Leipe, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Tatiana A. Tatusova, Lukas Wagner, and Barbara A. Rapp: Database resources of the National Center for Biotechnology Information
Nucl. Acids Res. 2001 29: 11-16; doi:10.1093/nar/29.1.11 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Evelyn Camon, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Vincent Lombard, Rodrigo Lopez, Helen Parkinson, Nicole Redaschi, Peter Sterk, Peter Stoehr, and Mary Ann Tuli: The EMBL nucleotide sequence database
Nucl. Acids Res. 2001 29: 17-21; doi:10.1093/nar/29.1.17 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Roman L. Tatusov, Darren A. Natale, Igor V. Garkavtsev, Tatiana A. Tatusova, Uma T. Shankavaram, Bachoti S. Rao, Boris Kiryutin, Michael Y. Galperin, Natalie D. Fedorova, and Eugene V. Koonin: The COG database: new developments in phylogenetic classification of proteins from complete genomes
Nucl. Acids Res. 2001 29: 22-28; doi:10.1093/nar/29.1.22 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Winona C. Barker, John S. Garavelli, Zhenglin Hou, Hongzhan Huang, Robert S. Ledley, Peter B. McGarvey, Hans-Werner Mewes, Bruce C. Orcutt, Friedhelm Pfeiffer, Akira Tsugita, C. R. Vinayaka, Chunlin Xiao, Lai-Su L. Yeh, and Cathy Wu: Protein Information Resource: a community resource for expert annotation of protein data
Nucl. Acids Res. 2001 29: 29-32; doi:10.1093/nar/29.1.29 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Evgenia V. Kriventseva, Wolfgang Fleischmann, Evgeni M. Zdobnov, and Rolf Apweiler: CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins
Nucl. Acids Res. 2001 29: 33-36; doi:10.1093/nar/29.1.33 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, E. Birney, M. Biswas, P. Bucher, L. Cerutti, F. Corpet, M. D. R. Croning, R. Durbin, L. Falquet, W. Fleischmann, J. Gouzy, H. Hermjakob, N. Hulo, I. Jonassen, D. Kahn, A. Kanapin, Y. Karavidopoulou, R. Lopez, B. Marx, N. J. Mulder, T. M. Oinn, M. Pagni, F. Servant, C. J. A. Sigrist, and E. M. Zdobnov: The InterPro database, an integrated documentation resource for protein families, domains and functional sites
Nucl. Acids Res. 2001 29: 37-40; doi:10.1093/nar/29.1.37 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Daniel H. Haft, Brendan J. Loftus, Delwood L. Richardson, Fan Yang, Jonathan A. Eisen, Ian T. Paulsen, and Owen White: TIGRFAMs: a protein family resource for the functional identification of proteins
Nucl. Acids Res. 2001 29: 41-43; doi:10.1093/nar/29.1.41 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Rolf Apweiler, Margaret Biswas, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola Mulder, Isabelle Phan, and Evgeni Zdobnov: Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes
Nucl. Acids Res. 2001 29: 44-48; doi:10.1093/nar/29.1.44 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Kevin A. T. Silverstein, Elizabeth Shoop, James E. Johnson, Alan Kilian, John L. Freeman, Timothy M. Kunau, Ihab A. Awad, Margaret Mayer, and Ernest F. Retzel: The MetaFam Server: a comprehensive protein family resource
Nucl. Acids Res. 2001 29: 49-51; doi:10.1093/nar/29.1.49 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Cathy H. Wu, Chunlin Xiao, Zhenglin Hou, Hongzhan Huang, and Winona C. Barker: iProClass: an integrated, comprehensive and annotated protein classification database
Nucl. Acids Res. 2001 29: 52-54; doi:10.1093/nar/29.1.52 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Sabine Dietmann, Jong Park, Cedric Notredame, Andreas Heger, Michael Lappe, and Liisa Holm: A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3
Nucl. Acids Res. 2001 29: 55-57; doi:10.1093/nar/29.1.55 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

János Murvai, Kristian Vlahovicek, Endre Barta, and Sándor Pongor: The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments
Nucl. Acids Res. 2001 29: 58-60; doi:10.1093/nar/29.1.58 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

S. Balaji, S. Sujatha, S. Sai Chetan Kumar, and N. Srinivasan: PALI—a database of Phylogeny and ALIgnment of homologous protein structures
Nucl. Acids Res. 2001 29: 61-65; doi:10.1093/nar/29.1.61 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

The Plasmodium Genome Database Collaborative: PlasmoDB: An integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data
Nucl. Acids Res. 2001 29: 66-69; doi:10.1093/nar/29.1.66 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Junichi Watanabe, Masahide Sasaki, Yutaka Suzuki, and Sumio Sugano: FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum
Nucl. Acids Res. 2001 29: 70-71; doi:10.1093/nar/29.1.70 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Heladia Salgado, Alberto Santos-Zavaleta, Socorro Gama-Castro, Dulce Millán-Zárate, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Ernesto Pérez-Rueda, César Bonavides-Martínez, and Julio Collado-Vides: RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12
Nucl. Acids Res. 2001 29: 72-74; doi:10.1093/nar/29.1.72 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Maria C. Costanzo, Matthew E. Crawford, Jodi E. Hirschman, Janice E. Kranz, Philip Olsen, Laura S. Robertson, Marek S. Skrzypek, Burkhard R. Braun, Kelley Lennon Hopkins, Pinar Kondu, Carey Lengieza, Jodi E. Lew-Smith, Michael Tillberg, and James I. Garrels: YPD^TM, PombePD^TM and WormPD^TM: model organism volumes of the BioKnowledge^TM Library, an integrated resource for protein information
Nucl. Acids Res. 2001 29: 75-79; doi:10.1093/nar/29.1.75 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Catherine A. Ball, Heng Jin, Gavin Sherlock, Shuai Weng, John C. Matese, Rey Andrada, Gail Binkley, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Laurie Issel-Tarver, Mark Schroeder, David Botstein, and J. Michael Cherry: Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data
Nucl. Acids Res. 2001 29: 80-81; doi:10.1093/nar/29.1.80 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Lincoln Stein, Paul Sternberg, Richard Durbin, Jean Thierry-Mieg, and John Spieth: WormBase: network access to the genome and biology of Caenorhabditis elegans
Nucl. Acids Res. 2001 29: 82-86; doi:10.1093/nar/29.1.82 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Judy Sprague, Eckehard Doerry, Sarah Douglas, and Monte Westerfield: The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research
Nucl. Acids Res. 2001 29: 87-90; doi:10.1093/nar/29.1.87 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Judith A. Blake, Janan T. Eppig, Joel E. Richardson, Carol J. Bult, and J. A. Kadin: The Mouse Genome Database (MGD): integration nexus for the laboratory mouse
Nucl. Acids Res. 2001 29: 91-94; doi:10.1093/nar/29.1.91 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Carol J. Bult, Debra M. Krupke, Dieter Näf, John P. Sundberg, and Janan T. Eppig: Web-based access to mouse models of human cancers: the Mouse Tumor Biology (MTB) Database
Nucl. Acids Res. 2001 29: 95-97; doi:10.1093/nar/29.1.95 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Martin Ringwald, Janan T. Eppig, Dale A. Begley, John P. Corradi, Ingeborg J. McCright, Terry F. Hayamizu, David P. Hill, James A. Kadin, and Joel E. Richardson: The Mouse Gene Expression Database (GXD)
Nucl. Acids Res. 2001 29: 98-101; doi:10.1093/nar/29.1.98 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Eva Huala, Allan W. Dickerman, Margarita Garcia-Hernandez, Danforth Weems, Leonore Reiser, Frank LaFond, David Hanley, Donald Kiphart, Mingzhe Zhuang, Wen Huang, Lukas A. Mueller, Debika Bhattacharyya, Devaki Bhaya, Bruno W. Sobral, William Beavis, David W. Meinke, Christopher D. Town, Chris Somerville, and Seung Yon Rhee: The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant
Nucl. Acids Res. 2001 29: 102-105; doi:10.1093/nar/29.1.102 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Jian Hu, Chris Mungall, Andy Law, Richard Papworth, J. Paul Nelson, Alison Brown, Irene Simpson, Shirley Leckie, David W. Burt, Alan L. Hillyard, and Alan L. Archibald: The ARKdb: genome databases for farmed and other animals
Nucl. Acids Res. 2001 29: 106-110; doi:10.1093/nar/29.1.106 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Michael Gribskov, Fariba Fana, Jeffrey Harper, Debra A. Hope, Alice C. Harmon, Douglas W. Smith, Frans E. Tax, and Guangfa Zhang: PlantsP: a functional genomics database for plant phosphorylation
Nucl. Acids Res. 2001 29: 111-113; doi:10.1093/nar/29.1.111 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Callum J. Bell, Richard A. Dixon, Andrew D. Farmer, Raul Flores, Jeff Inman, Robert A. Gonzales, Maria J. Harrison, Nancy L. Paiva, Angela D. Scott, Jennifer W. Weller, and Gregory D. May: The Medicago Genome Initiative: a model legume database
Nucl. Acids Res. 2001 29: 114-117; doi:10.1093/nar/29.1.114 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Carl A. Price and Ellen M. Reardon: Mendel, a database of nomenclature for sequenced plant genes
Nucl. Acids Res. 2001 29: 118-119; doi:10.1093/nar/29.1.118 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

David Lonsdale, Mark Crowe, Benjamin Arnold, and Benedict C. Arnold: Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names
Nucl. Acids Res. 2001 29: 120-122; doi:10.1093/nar/29.1.120 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Jeremy D. Peterson, Lowell A. Umayam, Tanja Dickinson, Erin K. Hickey, and Owen White: The Comprehensive Microbial Resource
Nucl. Acids Res. 2001 29: 123-125; doi:10.1093/nar/29.1.123 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Axel Bernal, Uy Ear, and Nikos Kyrpides: Genomes OnLine Database (GOLD): a monitor of genome projects world-wide
Nucl. Acids Res. 2001 29: 126-127; doi:10.1093/nar/29.1.126 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Nelli Shimko, Lin Liu, B. Franz Lang, and Gertraud Burger: GOBASE: the organelle genome database
Nucl. Acids Res. 2001 29: 128-132; doi:10.1093/nar/29.1.128 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

M. Mar Albà, David Lee, Frances M. G. Pearl, Adrian J. Shepherd, Nigel Martin, Christine A. Orengo, and Paul Kellam: VIDA: a virus database system for the organization of animal virus genome open reading frames
Nucl. Acids Res. 2001 29: 133-136; doi:10.1093/nar/29.1.133 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Kim D. Pruitt and Donna R. Maglott: RefSeq and LocusLink: NCBI gene-centered resources
Nucl. Acids Res. 2001 29: 137-140; doi:10.1093/nar/29.1.137 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Shaying Zhao: A comprehensive BAC resource
Nucl. Acids Res. 2001 29: 141-143; doi:10.1093/nar/29.1.141 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Michael Morley, Melissa Arcaro, Joshua Burdick, Raluca Yonescu, Thomas Reid, Ilan R. Kirsch, and Vivian G. Cheung: GenMapDB: a database of mapped human BAC clones
Nucl. Acids Res. 2001 29: 144-147; doi:10.1093/nar/29.1.144 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Marco Pagni, Christian Iseli, Thomas Junier, Laurent Falquet, Victor Jongeneel, and Philipp Bucher: trEST, trGEN and Hits: access to databases of predicted protein sequences
Nucl. Acids Res. 2001 29: 148-151; doi:10.1093/nar/29.1.148 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Gavin Sherlock, Tina Hernandez-Boussard, Andrew Kasarskis, Gail Binkley, John C. Matese, Selina S. Dwight, Miroslava Kaloper, Shuai Weng, Heng Jin, Catherine A. Ball, Michael B. Eisen, Paul T. Spellman, Patrick O. Brown, David Botstein, and J. Michael Cherry: The Stanford Microarray Database
Nucl. Acids Res. 2001 29: 152-155; doi:10.1093/nar/29.1.152 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Jun Sese, Hitoshi Nikaidou, Shoko Kawamoto, Yuichi Minesaki, Shinichi Morishita, and Kousaku Okubo: BodyMap incorporated PCR-based expression profiling data and a gene ranking system
Nucl. Acids Res. 2001 29: 156-158; doi:10.1093/nar/29.1.156 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

John Quackenbush, Jennifer Cho, Daniel Lee, Feng Liang, Ingeborg Holt, Svetlana Karamycheva, Babak Parvizi, Geo Pertea, Razvan Sultana, and Joseph White: The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
Nucl. Acids Res. 2001 29: 159-164; doi:10.1093/nar/29.1.159 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Patricia Rodriguez-Tomé and Philip Lijnzaad: RHdb: the Radiation Hybrid database
Nucl. Acids Res. 2001 29: 165-166; doi:10.1093/nar/29.1.165 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Fabrizio Damiano, Raffaele Gallerani, Sabino Liuni, Flavio Licciulli, and Luigi R. Ceci: PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes
Nucl. Acids Res. 2001 29: 167-168; doi:10.1093/nar/29.1.167 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, and Tore Samuelsson: SRPDB (Signal Recognition Particle Database)
Nucl. Acids Res. 2001 29: 169-170; doi:10.1093/nar/29.1.169 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Bjarne Knudsen, Jacek Wower, Christian Zwieb, and Jan Gorodkin: tmRDB (tmRNA database)
Nucl. Acids Res. 2001 29: 171-172; doi:10.1093/nar/29.1.171 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Bonnie L. Maidak, James R. Cole, Timothy G. Lilburn, Charles T. Parker, Jr, Paul R. Saxman, Ryan J. Farris, George M. Garrity, Gary J. Olsen, Thomas M. Schmidt, and James M. Tiedje: The RDP-II (Ribosomal Database Project)
Nucl. Acids Res. 2001 29: 173-174; doi:10.1093/nar/29.1.173 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Jan Wuyts, Peter De Rijk, Yves Van de Peer, Tina Winkelmans, and Rupert De Wachter: The European Large Subunit Ribosomal RNA Database
Nucl. Acids Res. 2001 29: 175-177; doi:10.1093/nar/29.1.175 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Jesús García-Martínez, Ignacio Bescós, Jesús Javier Rodríguez-Sala, and Francisco Rodríguez-Valera: RISSC: a novel database for ribosomal 16S–23S RNA genes spacer regions
Nucl. Acids Res. 2001 29: 178-180; doi:10.1093/nar/29.1.178 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Joel A. Klappenbach, Paul R. Saxman, James R. Cole, and Thomas M. Schmidt: rrndb: the Ribosomal RNA Operon Copy Number Database
Nucl. Acids Res. 2001 29: 181-184; doi:10.1093/nar/29.1.181 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Henrik T. Yudate, Makiko Suwa, Ryotaro Irie, Hiroshi Matsui, Tetsuo Nishikawa, Yoshitaka Nakamura, Daisuke Yamaguchi, Zhang Zhi Peng, Tomoyuki Yamamoto, Keiichi Nagai, Koji Hayashi, Tetsuji Otsuki, Tomoyasu Sugiyama, Toshio Ota, Yutaka Suzuki, Sumio Sugano, Takao Isogai, and Yasuhiko Masuho: HUNT: launch of a full-length cDNA database from the Helix Research Institute
Nucl. Acids Res. 2001 29: 185-188; doi:10.1093/nar/29.1.185 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Volker A. Erdmann, Miroslawa Z. Barciszewska, Maciej Szymanski, Abraham Hochberg, Nathan de Groot, and Jan Barciszewski: The non-coding RNAs as riboregulators
Nucl. Acids Res. 2001 29: 189-193; doi:10.1093/nar/29.1.189 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

F. H. D. van Batenburg, A. P. Gultyaev, and C. W. A. Pleij: PseudoBase: structural information on RNA pseudoknots
Nucl. Acids Res. 2001 29: 194-195; doi:10.1093/nar/29.1.194 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Stefan Gräf, Dirk Strothmann, Stefan Kurtz, and Gerhard Steger: HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns
Nucl. Acids Res. 2001 29: 196-198; doi:10.1093/nar/29.1.196 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

John S. Garavelli, Zhenglin Hou, Nagarajan Pattabiraman, and Robert M. Stephens: The RESID Database of protein structure modifications and the NRL-3D Sequence–Structure Database
Nucl. Acids Res. 2001 29: 199-201; doi:10.1093/nar/29.1.199 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Jimmy Y. Huang and Douglas L. Brutlag: The EMOTIF database
Nucl. Acids Res. 2001 29: 202-204; doi:10.1093/nar/29.1.202 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

George Johnson and Tai Te Wu: Kabat Database and its applications: future directions
Nucl. Acids Res. 2001 29: 205-206; doi:10.1093/nar/29.1.205 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Marie-Paule Lefranc: IMGT, the international ImMunoGeneTics database
Nucl. Acids Res. 2001 29: 207-209; doi:10.1093/nar/29.1.207 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

James Robinson, Matthew J. Waller, Peter Parham, Julia G. Bodmer, and Steven G. E. Marsh: IMGT/HLA Database—a sequence database for the human major histocompatibility complex
Nucl. Acids Res. 2001 29: 210-213; doi:10.1093/nar/29.1.210 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

T. N. Bhat, Philip Bourne, Zukang Feng, Gary Gilliland, Shri Jain, Veerasamy Ravichandran, Bohdan Schneider, Kata Schneider, Narmada Thanki, Helge Weissig, John Westbrook, and Helen M. Berman: The PDB data uniformity project
Nucl. Acids Res. 2001 29: 214-218; doi:10.1093/nar/29.1.214 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Tamotsu Noguchi, Hideo Matsuda, and Yutaka Akiyama: PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)
Nucl. Acids Res. 2001 29: 219-220; doi:10.1093/nar/29.1.219 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Roman A. Laskowski: PDBsum: summaries and analyses of PDB structures
Nucl. Acids Res. 2001 29: 221-222; doi:10.1093/nar/29.1.221 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Frances M. G. Pearl, Nigel Martin, James E. Bray, Daniel W. A. Buchan, Andrew P. Harrison, David Lee, Gabrielle A. Reeves, Adrian J. Shepherd, Ian Sillitoe, Annabel E. Todd, Janet M. Thornton, and Christine A. Orengo: A rapid classification protocol for the CATH Domain Database to support structural genomics
Nucl. Acids Res. 2001 29: 223-227; doi:10.1093/nar/29.1.223 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Ilya N. Shindyalov and Philip E. Bourne: A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm
Nucl. Acids Res. 2001 29: 228-229; doi:10.1093/nar/29.1.228 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Wing Lok Abe Kurtz Chiu, Chun Ngai Sze, Lai Nang Ip, Sze Ki Chan, and Steve Chik Fun Au-Yeung: NTDB: Thermodynamic Database for Nucleic Acids
Nucl. Acids Res. 2001 29: 230-233; doi:10.1093/nar/29.1.230 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Alan Christoffels, Antoine van Gelder, Gary Greyling, Robert Miller, Tania Hide, and Winston Hide: STACK: Sequence Tag Alignment and Consensus Knowledgebase
Nucl. Acids Res. 2001 29: 234-238; doi:10.1093/nar/29.1.234 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Ioannis Xenarios, Esteban Fernandez, Lukasz Salwinski, Xiaoqun Joyce Duan, Michael J. Thompson, Edward M. Marcotte, and David Eisenberg: DIP: The Database of Interacting Proteins: 2001 update
Nucl. Acids Res. 2001 29: 239-241; doi:10.1093/nar/29.1.239 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Gary D. Bader, Ian Donaldson, Cheryl Wolting, B. F. Francis Ouellette, Tony Pawson, and Christopher W. V. Hogue: BIND—The Biomolecular Interaction Network Database
Nucl. Acids Res. 2001 29: 242-245; doi:10.1093/nar/29.1.242 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Tala Bakheet, Mathias Frevel, Bryan R. G. Williams, William Greer, and Khalid S. A. Khabar: ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins
Nucl. Acids Res. 2001 29: 246-254; doi:10.1093/nar/29.1.246 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

M. Burset, I. A. Seledtsov, and V. V. Solovyev: SpliceDB: database of canonical and non-canonical mammalian splice sites
Nucl. Acids Res. 2001 29: 255-259; doi:10.1093/nar/29.1.255 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Hongkai Ji, Qing Zhou, Fang Wen, Huiyu Xia, Xin Lu, and Yanda Li: AsMamDB: an alternative splice database of mammals
Nucl. Acids Res. 2001 29: 260-263; doi:10.1093/nar/29.1.260 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Pavel V. Baranov, Olga L. Gurvich, Olivier Fayet, Marie Françoise Prère, W. Allen Miller, Raymond F. Gesteland, John F. Atkins, and Michael C. Giddings: RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression
Nucl. Acids Res. 2001 29: 264-267; doi:10.1093/nar/29.1.264 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Richard J. Roberts and Dana Macelis: REBASE—restriction enzymes and methylases
Nucl. Acids Res. 2001 29: 268-269; doi:10.1093/nar/29.1.268 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Christoph Grunau, Eric Renault, André Rosenthal, and Gérard Roizes: MethDB—a public database for DNA methylation data
Nucl. Acids Res. 2001 29: 270-274; doi:10.1093/nar/29.1.270 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Ian M. Morison, Croydon J. Paton, and Susan D. Cleverley: The imprinted gene and parent-of-origin effect database
Nucl. Acids Res. 2001 29: 275-276; doi:10.1093/nar/29.1.275 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Ruti Hershberg, Gill Bejerano, Alberto Santos-Zavaleta, and Hanah Margalit: PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites
Nucl. Acids Res. 2001 29: 277; doi:10.1093/nar/29.1.277 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Takahiro Ishii, Ken-ichi Yoshida, Goro Terai, Yasutaro Fujita, and Kenta Nakai: DBTBS: a database of Bacillus subtilis promoters and transcription factors
Nucl. Acids Res. 2001 29: 278-280; doi:10.1093/nar/29.1.278 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

E. Wingender, X. Chen, E. Fricke, R. Geffers, R. Hehl, I. Liebich, M. Krull, V. Matys, H. Michael, R. Ohnhäuser, M. Prüß, F. Schacherer, S. Thiele, and S. Urbach: The TRANSFAC system on gene expression regulation
Nucl. Acids Res. 2001 29: 281-283; doi:10.1093/nar/29.1.281 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Julia V. Ponomarenko, Dagmara P. Furman, Anatoly S. Frolov, Nikolay L. Podkolodny, Galina V. Orlova, Mikhail P. Ponomarenko, Nikolay A. Kolchanov, and Akinori Sarai: ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another
Nucl. Acids Res. 2001 29: 284-287; doi:10.1093/nar/29.1.284 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Maciej Szymanski, Marzanna A. Deniziak, and Jan Barciszewski: Aminoacyl-tRNA synthetases database
Nucl. Acids Res. 2001 29: 288-290; doi:10.1093/nar/29.1.288 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Sharmila Banerjee-Basu, Daniel W. Sink, and Andreas D. Baxevanis: The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information
Nucl. Acids Res. 2001 29: 291-293; doi:10.1093/nar/29.1.291 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Nicolas Le Novère and Jean-Pierre Changeux: LGICdb: the ligand-gated ion channel database
Nucl. Acids Res. 2001 29: 294-295; doi:10.1093/nar/29.1.294 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Rami Kantor, Rhoderick Machekano, Mathew J. Gonzales, Kathryn Dupnik, Jonathan M. Schapiro, and Robert W. Shafer: Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs
Nucl. Acids Res. 2001 29: 296-299; doi:10.1093/nar/29.1.296 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Alan E. Levine and David L. Steffen: OrCGDB: a database of genes involved in oral cancer
Nucl. Acids Res. 2001 29: 300-302; doi:10.1093/nar/29.1.300 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Jean-Loup Huret, Philippe Dessen, and Alain Bernheim: Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated
Nucl. Acids Res. 2001 29: 303-304; doi:10.1093/nar/29.1.303 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Olivier Cohen, Marie-Ange Mermet, and Jacques Demongeot: HC Forum®: a web site based on an international human cytogenetic database
Nucl. Acids Res. 2001 29: 305-307; doi:10.1093/nar/29.1.305 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

S. T. Sherry, M.-H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski, and K. Sirotkin: dbSNP: the NCBI database of genetic variation
Nucl. Acids Res. 2001 29: 308-311; doi:10.1093/nar/29.1.308 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Julia V. Ponomarenko, Tatyana I. Merkulova, Gennady V. Vasiliev, Zoya B. Levashova, Galina V. Orlova, Sergey V. Lavryushev, Oleg N. Fokin, Mikhail P. Ponomarenko, Anatoly S. Frolov, and Akinori Sarai: rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations
Nucl. Acids Res. 2001 29: 312-316; doi:10.1093/nar/29.1.312 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Michael V. Osier, Kei-Hoi Cheung, Judith R. Kidd, Andrew J. Pakstis, Perry L. Miller, and Kenneth K. Kidd: ALFRED: an allele frequency database for diverse populations and DNA polymorphisms—an update
Nucl. Acids Res. 2001 29: 317-319; doi:10.1093/nar/29.1.317 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Christian M. Ruitberg, Dennis J. Reeder, and John M. Butler: STRBase: a short tandem repeat DNA database for the human identity testing community
Nucl. Acids Res. 2001 29: 320-322; doi:10.1093/nar/29.1.320 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Anne Bahr, Julie D. Thompson, J.-C. Thierry, and Olivier Poch: BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations
Nucl. Acids Res. 2001 29: 323-326; doi:10.1093/nar/29.1.323 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Shinsei Minoshima, Susumu Mitsuyama, Masafumi Ohtsubo, Takashi Kawamura, Sachiko Ito, Sayumi Shibamoto, Fumiaki Ito, and Nobuyoshi Shimizu: The KMDB/MutationView: a mutation database for human disease genes
Nucl. Acids Res. 2001 29: 327-328; doi:10.1093/nar/29.1.327 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Wilfred W. Li, Boojala V. B. Reddy, Ilya N. Shindyalov, and Philip E. Bourne: CKAAPs DB: a conserved key amino acid positions database
Nucl. Acids Res. 2001 29: 329-331; doi:10.1093/nar/29.1.329 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Catherine A. Cooper, Mathew J. Harrison, Marc R. Wilkins, and Nicolle H. Packer: GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources
Nucl. Acids Res. 2001 29: 332-335; doi:10.1093/nar/29.1.332 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Eduardo Gonzalez-Couto, Brian Hayes, and Anne Danckaert: The life sciences Global Image Database (GID)
Nucl. Acids Res. 2001 29: 336-339; doi:10.1093/nar/29.1.336 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Lynda B. M. Ellis, C. Douglas Hershberger, Edward M. Bryan, and Lawrence P. Wackett: The University of Minnesota Biocatalysis/Biodegradation Database: emphasizing enzymes
Nucl. Acids Res. 2001 29: 340-343; doi:10.1093/nar/29.1.340 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Data] [Request Permissions]

Kanako Watanabe, James Nelson, Shigeaki Harayama, and Hiroaki Kasai: ICB database: the gyrB database for identification and classification of bacteria
Nucl. Acids Res. 2001 29: 344-345; doi:10.1093/nar/29.1.344 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

Florence Horn, Gerrit Vriend, and Fred E. Cohen: Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems
Nucl. Acids Res. 2001 29: 346-349; doi:10.1093/nar/29.1.346 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]

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