Nucleic Acids Research

Editorial:

EDITORIAL
Nucl. Acids Res. 2004 32: D1; doi:10.1093/nar/gkh142 [Extract] [FREE Full Text] [Print PDF]  

Articles:

Michael Y. Galperin

The Molecular Biology Database Collection: 2004 update
Nucl. Acids Res. 2004 32: D3-D22; doi:10.1093/nar/gkh143 [Abstract] [FREE Full Text] [Print PDF] [Database Listing]  

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

GenBank: update
Nucl. Acids Res. 2004 32: D23-D26; doi:10.1093/nar/gkh045 [Abstract] [FREE Full Text] [Print PDF]  

Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Maria Garcia-Pastor, Nicola Harte, Carola Kanz, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Peter Stoehr, Guenter Stoesser, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler

The EMBL Nucleotide Sequence Database
Nucl. Acids Res. 2004 32: D27-D30; doi:10.1093/nar/gkh120 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

S. Miyazaki, H. Sugawara, K. Ikeo, T. Gojobori, and Y. Tateno

DDBJ in the stream of various biological data
Nucl. Acids Res. 2004 32: D31-D34; doi:10.1093/nar/gkh127 [Abstract] [FREE Full Text] [Print PDF]  

David L. Wheeler, Deanna M. Church, Ron Edgar, Scott Federhen, Wolfgang Helmberg, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tugba O. Suzek, Tatiana A. Tatusova, and Lukas Wagner

Database resources of the National Center for Biotechnology Information: update
Nucl. Acids Res. 2004 32: D35-D40; doi:10.1093/nar/gkh073 [Abstract] [FREE Full Text] [Print PDF]  

H. W. Mewes, C. Amid, R. Arnold, D. Frishman, U. Güldener, G. Mannhaupt, M. Münsterkötter, P. Pagel, N. Strack, V. Stümpflen, J. Warfsmann, and A. Ruepp

MIPS: analysis and annotation of proteins from whole genomes
Nucl. Acids Res. 2004 32: D41-D44; doi:10.1093/nar/gkh092 [Abstract] [FREE Full Text] [Print PDF]  

Raphaël Leplae, Aline Hebrant, Shoshana J. Wodak, and Ariane Toussaint

ACLAME: A CLAssification of Mobile genetic Elements
Nucl. Acids Res. 2004 32: D45-D49; doi:10.1093/nar/gkh084 [Abstract] [FREE Full Text] [Print PDF]  

Jan Paces, Adam Pavlícek, Radek Zika, Vladimir V. Kapitonov, Jerzy Jurka, and Václav Paces

HERVd: the Human Endogenous RetroViruses Database: update
Nucl. Acids Res. 2004 32: D50; doi:10.1093/nar/gkh075 [Abstract] [FREE Full Text] [Print PDF]  

Thierry-Pascal Baum, Nicolas Pasqual, Florence Thuderoz, Vivien Hierle, Denys Chaume, Marie-Paule Lefranc, Evelyne Jouvin-Marche, Patrice-Noël Marche, and Jacques Demongeot

IMGT/GeneInfo: enhancing V(D)J recombination database accessibility
Nucl. Acids Res. 2004 32: D51-D54; doi:10.1093/nar/gkh041 [Abstract] [FREE Full Text] [Print PDF]  

Yogita Mantri and Kelly P. Williams

Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
Nucl. Acids Res. 2004 32: D55-D58; doi:10.1093/nar/gkh059 [Abstract] [FREE Full Text] [Print PDF]  

Vivek Gopalan, Tin Wee Tan, Bernett T. K. Lee, and Shoba Ranganathan

Xpro: database of eukaryotic protein-encoding genes
Nucl. Acids Res. 2004 32: D59-D63; doi:10.1093/nar/gkh051 [Abstract] [FREE Full Text] [Print PDF]  

T. A. Thanaraj, Stefan Stamm, Francis Clark, Jean-Jack Riethoven, Vincent Le Texier, and Juha Muilu

ASD: the Alternative Splicing Database
Nucl. Acids Res. 2004 32: D64-D69; doi:10.1093/nar/gkh030 [Abstract] [FREE Full Text] [Print PDF]  

Heike Pospisil, Alexander Herrmann, Ralf H. Bortfeldt, and Jens G. Reich

EASED: Extended Alternatively Spliced EST Database
Nucl. Acids Res. 2004 32: D70-D74; doi:10.1093/nar/gkh136 [Abstract] [FREE Full Text] [Print PDF]  

Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, and Kenta Nakai

DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics
Nucl. Acids Res. 2004 32: D75-D77; doi:10.1093/nar/gkh074 [Abstract] [FREE Full Text] [Print PDF]  

Yutaka Suzuki, Riu Yamashita, Sumio Sugano, and Kenta Nakai

DBTSS, DataBase of Transcriptional Start Sites: progress report 2004
Nucl. Acids Res. 2004 32: D78-D81; doi:10.1093/nar/gkh076 [Abstract] [FREE Full Text] [Print PDF]  

Christoph D. Schmid, Viviane Praz, Mauro Delorenzi, Rouaïda Périer, and Philipp Bucher

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension
Nucl. Acids Res. 2004 32: D82-D85; doi:10.1093/nar/gkh122 [Abstract] [FREE Full Text] [Print PDF]  

Twyla T. Pohar, Hao Sun, and Ramana V. Davuluri

HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development
Nucl. Acids Res. 2004 32: D86-D90; doi:10.1093/nar/gkh056 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Albin Sandelin, Wynand Alkema, Pär Engström, Wyeth W. Wasserman, and Boris Lenhard

JASPAR: an open-access database for eukaryotic transcription factor binding profiles
Nucl. Acids Res. 2004 32: D91-D94; doi:10.1093/nar/gkh012 [Abstract] [FREE Full Text] [Print PDF]  

Jennifer F. Lee, Jay R. Hesselberth, Lauren Ancel Meyers, and Andrew D. Ellington

Aptamer Database
Nucl. Acids Res. 2004 32: D95-D100; doi:10.1093/nar/gkh094 [Abstract] [FREE Full Text] [Print PDF]  

Jan Wuyts, Guy Perrière, and Yves Van de Peer

The European ribosomal RNA database
Nucl. Acids Res. 2004 32: D101-D103; doi:10.1093/nar/gkh065 [Abstract] [FREE Full Text] [Print PDF]  

Pulcherie Gueneau de Novoa and Kelly P. Williams

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts
Nucl. Acids Res. 2004 32: D104-D108; doi:10.1093/nar/gkh102 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Sam Griffiths-Jones

The microRNA Registry
Nucl. Acids Res. 2004 32: D109-D111; doi:10.1093/nar/gkh023 [Abstract] [FREE Full Text] [Print PDF]  

Cathy H. Wu, Anastasia Nikolskaya, Hongzhan Huang, Lai-Su L. Yeh, Darren A. Natale, C. R. Vinayaka, Zhang-Zhi Hu, Raja Mazumder, Sandeep Kumar, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Leslie Arminski, Yongxing Chen, Jian Zhang, Jorge Louie Cardenas, Sehee Chung, Jorge Castro-Alvear, Georgi Dinkov, and Winona C. Barker

PIRSF: family classification system at the Protein Information Resource
Nucl. Acids Res. 2004 32: D112-D114; doi:10.1093/nar/gkh097 [Abstract] [FREE Full Text] [Print PDF]  

Rolf Apweiler, Amos Bairoch, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria J. Martin, Darren A. Natale, Claire O’Donovan, Nicole Redaschi, and Lai-Su L. Yeh

UniProt: the Universal Protein knowledgebase
Nucl. Acids Res. 2004 32: D115-D119; doi:10.1093/nar/gkh131 [Abstract] [FREE Full Text] [Print PDF]  

K. Abdulla Bava, M. Michael Gromiha, Hatsuho Uedaira, Koji Kitajima, and Akinori Sarai

ProTherm, version 4.0: thermodynamic database for proteins and mutants
Nucl. Acids Res. 2004 32: D120-D121; doi:10.1093/nar/gkh082 [Abstract] [FREE Full Text] [Print PDF]  

Tao Guo, Sujun Hua, Xinglai Ji, and Zhirong Sun

DBSubLoc: database of protein subcellular localization
Nucl. Acids Res. 2004 32: D122-D124; doi:10.1093/nar/gkh109 [Abstract] [FREE Full Text] [Print PDF]  

S. A. Fernando, P. Selvarani, Soma Das, Ch. Kiran Kumar, Sukanta Mondal, S. Ramakumar, and K. Sekar

THGS: a web-based database of Transmembrane Helices in Genome Sequences
Nucl. Acids Res. 2004 32: D125-D128; doi:10.1093/nar/gkh130 [Abstract] [FREE Full Text] [Print PDF]  

Craig T. Porter, Gail J. Bartlett, and Janet M. Thornton

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
Nucl. Acids Res. 2004 32: D129-D133; doi:10.1093/nar/gkh028 [Abstract] [FREE Full Text] [Print PDF]  

Nicolas Hulo, Christian J. A. Sigrist, Virginie Le Saux, Petra S. Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, and Amos Bairoch

Recent improvements to the PROSITE database
Nucl. Acids Res. 2004 32: D134-D137; doi:10.1093/nar/gkh044 [Abstract] [FREE Full Text] [Print PDF]  

Alex Bateman, Lachlan Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, and Sean R. Eddy

The Pfam protein families database
Nucl. Acids Res. 2004 32: D138-D141; doi:10.1093/nar/gkh121 [Abstract] [FREE Full Text] [Print PDF]  

Ivica Letunic, Richard R. Copley, Steffen Schmidt, Francesca D. Ciccarelli, Tobias Doerks, Jörg Schultz, Chris P. Ponting, and Peer Bork

SMART 4.0: towards genomic data integration
Nucl. Acids Res. 2004 32: D142-D144; doi:10.1093/nar/gkh088 [Abstract] [FREE Full Text] [Print PDF]  

Thierry Hotelier, Ludovic Renault, Xavier Cousin, Vincent Negre, Pascale Marchot, and Arnaud Chatonnet

ESTHER, the database of the /ß-hydrolase fold superfamily of proteins
Nucl. Acids Res. 2004 32: D145-D147; doi:10.1093/nar/gkh141 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

David A. Lee, Sandrine Fefeu, Adrian A. Edo-Ukeh, Christine A. Orengo, and Christine Slingsby

EyeSite: a semi-automated database of protein families in the eye
Nucl. Acids Res. 2004 32: D148-D152; doi:10.1093/nar/gkh090 [Abstract] [FREE Full Text] [Print PDF]  

A. Krupa, K. R. Abhinandan, and N. Srinivasan

KinG: a database of protein kinases in genomes
Nucl. Acids Res. 2004 32: D153-D155; doi:10.1093/nar/gkh019 [Abstract] [FREE Full Text] [Print PDF]  

Jean-Christophe Gelly, Jérôme Gracy, Quentin Kaas, Dung Le-Nguyen, Annie Heitz, and Laurent Chiche

The KNOTTIN website and database: a new information system dedicated to the knottin scaffold
Nucl. Acids Res. 2004 32: D156-D159; doi:10.1093/nar/gkh015 [Abstract] [FREE Full Text] [Print PDF]  

Neil D. Rawlings, Dominic P. Tolle, and Alan J. Barrett

MEROPS: the peptidase database
Nucl. Acids Res. 2004 32: D160-D164; doi:10.1093/nar/gkh071 [Abstract] [FREE Full Text] [Print PDF]  

David Ruau, Jorge Duarte, Tarik Ourjdal, Guy Perrière, Vincent Laudet, and Marc Robinson-Rechavi

Update of NUREBASE: nuclear hormone receptor functional genomics
Nucl. Acids Res. 2004 32: D165-D167; doi:10.1093/nar/gkh062 [Abstract] [FREE Full Text] [Print PDF]  

Akihiro Nakao, Maki Yoshihama, and Naoya Kenmochi

RPG: the Ribosomal Protein Gene database
Nucl. Acids Res. 2004 32: D168-D170; doi:10.1093/nar/gkh004 [Abstract] [FREE Full Text] [Print PDF]  

Antoni Hermoso, Daniel Aguilar, Francesc X. Aviles, and Enrique Querol

TrSDB: a proteome database of transcription factors
Nucl. Acids Res. 2004 32: D171-D173; doi:10.1093/nar/gkh101 [Abstract] [FREE Full Text] [Print PDF]  

Michael M. Hoffman, Maksim A. Khrapov, J. Colin Cox, Jianchao Yao, Lingnan Tong, and Andrew D. Ellington

AANT: the Amino Acid–Nucleotide Interaction Database
Nucl. Acids Res. 2004 32: D174-D181; doi:10.1093/nar/gkh128 [Abstract] [FREE Full Text] [Print PDF]  

Makio Tamura, Donna K. Hendrix, Peter S. Klosterman, Nancy R. B. Schimmelman, Steven E. Brenner, and Stephen R. Holbrook

SCOR: Structural Classification of RNA, version 2.0
Nucl. Acids Res. 2004 32: D182-D184; doi:10.1093/nar/gkh080 [Abstract] [FREE Full Text] [Print PDF]  

Jordi Espadaler, Narcis Fernandez-Fuentes, Antonio Hermoso, Enrique Querol, Francesc X. Aviles, Michael J. E. Sternberg, and Baldomero Oliva

ArchDB: automated protein loop classification as a tool for structural genomics
Nucl. Acids Res. 2004 32: D185-D188; doi:10.1093/nar/gkh002 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

John-Marc Chandonia, Gary Hon, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, and Steven E. Brenner

The ASTRAL Compendium in 2004
Nucl. Acids Res. 2004 32: D189-D192; doi:10.1093/nar/gkh034 [Abstract] [FREE Full Text] [Print PDF]  

R. Aroul Selvam and Rajkumar Sasidharan

DomIns: a web resource for domain insertions in known protein structures
Nucl. Acids Res. 2004 32: D193-D195; doi:10.1093/nar/gkh047 [Abstract] [FREE Full Text] [Print PDF]  

Liam J. McGuffin, Stefano A. Street, Kevin Bryson, Søren-Aksel Sørensen, and David T. Jones

The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms
Nucl. Acids Res. 2004 32: D196-D199; doi:10.1093/nar/gkh043 [Abstract] [FREE Full Text] [Print PDF]  

A. Vinayagam, G. Pugalenthi, R. Rajesh, and R. Sowdhamini

DSDBASE: a consortium of native and modelled disulphide bonds in proteins
Nucl. Acids Res. 2004 32: D200-D202; doi:10.1093/nar/gkh026 [Abstract] [FREE Full Text] [Print PDF]  

Lucy A. Stebbings and Kenji Mizuguchi

HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database
Nucl. Acids Res. 2004 32: D203-D207; doi:10.1093/nar/gkh027 [Abstract] [FREE Full Text] [Print PDF]  

Quentin Kaas, Manuel Ruiz, and Marie-Paule Lefranc

IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data
Nucl. Acids Res. 2004 32: D208-D210; doi:10.1093/nar/gkh042 [Abstract] [FREE Full Text] [Print PDF]  

A. Golovin, T. J. Oldfield, J. G. Tate, S. Velankar, G. J. Barton, H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Hussain, J. M. C. Ionides, M. John, P. A. Keller, E. Krissinel, P. McNeil, A. Naim, R. Newman, A. Pajon, J. Pineda, A. Rachedi, J. Copeland, A. Sitnov, S. Sobhany, A. Suarez-Uruena, G. J. Swaminathan, M. Tagari, S. Tromm, W. Vranken, and K. Henrick

E-MSD: an integrated data resource for bioinformatics
Nucl. Acids Res. 2004 32: D211-D216; doi:10.1093/nar/gkh078 [Abstract] [FREE Full Text] [Print PDF]  

Ursula Pieper, Narayanan Eswar, Hannes Braberg, M. S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Marti-Renom, Andras Fiser, Ben Webb, Daniel Greenblatt, Conrad C. Huang, Thomas E. Ferrin, and Andrej Sali

MODBASE, a database of annotated comparative protein structure models, and associated resources
Nucl. Acids Res. 2004 32: D217-D222; doi:10.1093/nar/gkh095 [Abstract] [FREE Full Text] [Print PDF]  

Philip E. Bourne, Kenneth J. Addess, Wolfgang F. Bluhm, Li Chen, Nita Deshpande, Zukang Feng, Ward Fleri, Rachel Green, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Helge Weissig, John Westbrook, and Helen M. Berman

The distribution and query systems of the RCSB Protein Data Bank
Nucl. Acids Res. 2004 32: D223-D225; doi:10.1093/nar/gkh096 [Abstract] [FREE Full Text] [Print PDF]  

Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, and Alexey G. Murzin

SCOP database in 2004: refinements integrate structure and sequence family data
Nucl. Acids Res. 2004 32: D226-D229; doi:10.1093/nar/gkh039 [Abstract] [FREE Full Text] [Print PDF]  

Jürgen Kopp and Torsten Schwede

The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models
Nucl. Acids Res. 2004 32: D230-D234; doi:10.1093/nar/gkh008 [Abstract] [FREE Full Text] [Print PDF]  

Martin Madera, Christine Vogel, Sarah K. Kummerfeld, Cyrus Chothia, and Julian Gough

The SUPERFAMILY database in 2004: additions and improvements
Nucl. Acids Res. 2004 32: D235-D239; doi:10.1093/nar/gkh117 [Abstract] [FREE Full Text] [Print PDF]  

Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, and Manuela Helmer-Citterich

SURFACE: a database of protein surface regions for functional annotation
Nucl. Acids Res. 2004 32: D240-D244; doi:10.1093/nar/gkh054 [Abstract] [FREE Full Text] [Print PDF]  

Keiran Fleming, Arne Müller, Robert M. MacCallum, and Michael J. E. Sternberg

3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
Nucl. Acids Res. 2004 32: D245-D250; doi:10.1093/nar/gkh064 [Abstract] [FREE Full Text] [Print PDF]  

Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, and David R. Westhead

TOPS: an enhanced database of protein structural topology
Nucl. Acids Res. 2004 32: D251-D254; doi:10.1093/nar/gkh060 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Hester M. Wain, Michael J. Lush, Fabrice Ducluzeau, Varsha K. Khodiyar, and Sue Povey

Genew: the Human Gene Nomenclature Database, 2004 updates
Nucl. Acids Res. 2004 32: D255-D257; doi:10.1093/nar/gkh072 [Abstract] [FREE Full Text] [Print PDF]  

Gene Ontology Consortium

The Gene Ontology (GO) database and informatics resource
Nucl. Acids Res. 2004 32: D258-D261; doi:10.1093/nar/gkh036 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Evelyn Camon, Michele Magrane, Daniel Barrell, Vivian Lee, Emily Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, and Rolf Apweiler

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
Nucl. Acids Res. 2004 32: D262-D266; doi:10.1093/nar/gkh021 [Abstract] [FREE Full Text] [Print PDF]  

Olivier Bodenreider

The Unified Medical Language System (UMLS): integrating biomedical terminology
Nucl. Acids Res. 2004 32: D267-D270; doi:10.1093/nar/gkh061 [Abstract] [FREE Full Text] [Print PDF]  

Ren Zhang, Hong-Yu Ou, and Chun-Ting Zhang

DEG: a database of essential genes
Nucl. Acids Res. 2004 32: D271-D272; doi:10.1093/nar/gkh024 [Abstract] [FREE Full Text] [Print PDF]  

Karsten Suhre and Jean-Michel Claverie

FusionDB: a database for in-depth analysis of prokaryotic gene fusion events
Nucl. Acids Res. 2004 32: D273-D276; doi:10.1093/nar/gkh053 [Abstract] [FREE Full Text] [Print PDF]  

Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Yasushi Okuno, and Masahiro Hattori

The KEGG resource for deciphering the genome
Nucl. Acids Res. 2004 32: D277-D280; doi:10.1093/nar/gkh063 [Abstract] [FREE Full Text] [Print PDF]  

Naomi Siew, Yaniv Azaria, and Daniel Fischer

The ORFanage: an ORFan database
Nucl. Acids Res. 2004 32: D281-D283; doi:10.1093/nar/gkh116 [Abstract] [FREE Full Text] [Print PDF]  

Qinghu Ren, Katherine H. Kang, and Ian T. Paulsen

TransportDB: a relational database of cellular membrane transport systems
Nucl. Acids Res. 2004 32: D284-D288; doi:10.1093/nar/gkh016 [Abstract] [FREE Full Text] [Print PDF]  

Urmila Kulkarni-Kale, Shriram Bhosle, G. Sunitha Manjari, and A. S. Kolaskar

VirGen: a comprehensive viral genome resource
Nucl. Acids Res. 2004 32: D289-D292; doi:10.1093/nar/gkh098 [Abstract] [FREE Full Text] [Print PDF]  

Shan Sundararaj, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani, Paul Stothard, Michael Ellison, and David S. Wishart

The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
Nucl. Acids Res. 2004 32: D293-D295; doi:10.1093/nar/gkh108 [Abstract] [FREE Full Text] [Print PDF]  

Roy R. Chaudhuri, Arshad M. Khan, and Mark J. Pallen

coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics
Nucl. Acids Res. 2004 32: D296-D299; doi:10.1093/nar/gkh031 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Margrethe H. Serres, Sulip Goswami, and Monica Riley

GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins
Nucl. Acids Res. 2004 32: D300-D302; doi:10.1093/nar/gkh087 [Abstract] [FREE Full Text] [Print PDF]  

Heladia Salgado, Socorro Gama-Castro, Agustino Martínez-Antonio, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Martín Peralta-Gil, Delfino Garcia-Alonso, Verónica Jiménez-Jacinto, Alberto Santos-Zavaleta, César Bonavides-Martínez, and Julio Collado-Vides

RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
Nucl. Acids Res. 2004 32: D303-D306; doi:10.1093/nar/gkh140 [Abstract] [FREE Full Text] [Print PDF]  

Aurélien Barré, Antoine de Daruvar, and Alain Blanchard

MolliGen, a database dedicated to the comparative genomics of Mollicutes
Nucl. Acids Res. 2004 32: D307-D310; doi:10.1093/nar/gkh114 [Abstract] [FREE Full Text] [Print PDF]  

Karen R. Christie, Shuai Weng, Rama Balakrishnan, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, and J. Michael Cherry

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
Nucl. Acids Res. 2004 32: D311-D314; doi:10.1093/nar/gkh033 [Abstract] [FREE Full Text] [Print PDF]  

David Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski, and Jean-Luc Souciet for the Génolevures Consortium

Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts
Nucl. Acids Res. 2004 32: D315-D318; doi:10.1093/nar/gkh091 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Taro L. Saito, Miwaka Ohtani, Hiroshi Sawai, Fumi Sano, Ayaka Saka, Daisuke Watanabe, Masashi Yukawa, Yoshikazu Ohya, and Shinichi Morishita

SCMD: Saccharomyces cerevisiae Morphological Database
Nucl. Acids Res. 2004 32: D319-D322; doi:10.1093/nar/gkh113 [Abstract] [FREE Full Text] [Print PDF]  

Gaëlle Lelandais, Stéphane Le Crom, Frédéric Devaux, Stéphane Vialette, George M. Church, Claude Jacq, and Philippe Marc

yMGV: a cross-species expression data mining tool
Nucl. Acids Res. 2004 32: D323-D325; doi:10.1093/nar/gkh135 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Li Li, Jonathan Crabtree, Steve Fischer, Deborah Pinney, Christian J. Stoeckert, Jr, L. David Sibley, and David S. Roos

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
Nucl. Acids Res. 2004 32: D326-D328; doi:10.1093/nar/gkh112 [Abstract] [FREE Full Text] [Print PDF]  

Daniela Puiu, Shinichiro Enomoto, Gregory A. Buck, Mitchell S. Abrahamsen, and Jessica C. Kissinger

CryptoDB: the Cryptosporidium genome resource
Nucl. Acids Res. 2004 32: D329-D331; doi:10.1093/nar/gkh050 [Abstract] [FREE Full Text] [Print PDF]  

Lisa Kreppel, Petra Fey, Pascale Gaudet, Eric Just, Warren A. Kibbe, Rex L. Chisholm, and Alan R. Kimmel

dictyBase: a new Dictyostelium discoideum genome database
Nucl. Acids Res. 2004 32: D332-D333; doi:10.1093/nar/gkh138 [Abstract] [FREE Full Text] [Print PDF]  

Junichi Watanabe, Yutaka Suzuki, Masahide Sasaki, and Sumio Sugano

Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species
Nucl. Acids Res. 2004 32: D334-D338; doi:10.1093/nar/gkh115 [Abstract] [FREE Full Text] [Print PDF]  

Christiane Hertz-Fowler, Chris S. Peacock, Valerie Wood, Martin Aslett, Arnaud Kerhornou, Paul Mooney, Adrian Tivey, Matthew Berriman, Neil Hall, Kim Rutherford, Julian Parkhill, Alasdair C. Ivens, Marie-Adele Rajandream, and Bart Barrell

GeneDB: a resource for prokaryotic and eukaryotic organisms
Nucl. Acids Res. 2004 32: D339-D343; doi:10.1093/nar/gkh007 [Abstract] [FREE Full Text] [Print PDF]  

Michael Luchtan, Chetna Warade, D. Brent Weatherly, Wim M. Degrave, Rick L. Tarleton, and Jessica C. Kissinger

TcruziDB: an integrated Trypanosoma cruzi genome resource
Nucl. Acids Res. 2004 32: D344-D346; doi:10.1093/nar/gkh049 [Abstract] [FREE Full Text] [Print PDF]  

Franck Samson, Véronique Brunaud, Sylvain Duchêne, Yannick De Oliveira, Michel Caboche, Alain Lecharny, and Sébastien Aubourg

FLAGdb⁺⁺: a database for the functional analysis of the Arabidopsis genome
Nucl. Acids Res. 2004 32: D347-D350; doi:10.1093/nar/gkh134 [Abstract] [FREE Full Text] [Print PDF]  

S. Mohseni-Zadeh, A. Louis, P. Brézellec, and J.-L. Risler

PHYTOPROT: a database of clusters of plant proteins
Nucl. Acids Res. 2004 32: D351-D353; doi:10.1093/nar/gkh040 [Abstract] [FREE Full Text] [Print PDF]  

Qunfeng Dong, Shannon D. Schlueter, and Volker Brendel

PlantGDB, plant genome database and analysis tools
Nucl. Acids Res. 2004 32: D354-D359; doi:10.1093/nar/gkh046 [Abstract] [FREE Full Text] [Print PDF]  

Shu Ouyang and C. Robin Buell

The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants
Nucl. Acids Res. 2004 32: D360-D363; doi:10.1093/nar/gkh099 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Manuel Ruiz, Mathieu Rouard, Louis Marie Raboin, Marc Lartaud, Pierre Lagoda, and Brigitte Courtois

TropGENE-DB, a multi-tropical crop information system
Nucl. Acids Res. 2004 32: D364-D367; doi:10.1093/nar/gkh105 [Abstract] [FREE Full Text] [Print PDF]  

Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Lorenz Bülow, and Reinhard Hehl

AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
Nucl. Acids Res. 2004 32: D368-D372; doi:10.1093/nar/gkh017 [Abstract] [FREE Full Text] [Print PDF]  

Heiko Schoof, Rebecca Ernst, Vladimir Nazarov, Lukas Pfeifer, Hans-Werner Mewes, and Klaus F. X. Mayer

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics
Nucl. Acids Res. 2004 32: D373-D376; doi:10.1093/nar/gkh068 [Abstract] [FREE Full Text] [Print PDF]  

Wenming Zhao, Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, and Jun Wang

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
Nucl. Acids Res. 2004 32: D377-D382; doi:10.1093/nar/gkh085 [Abstract] [FREE Full Text] [Print PDF]  

Junshi Yazaki, Keiichi Kojima, Kouji Suzuki, Naoki Kishimoto, and Shoshi Kikuchi

The Rice PIPELINE: a unification tool for plant functional genomics
Nucl. Acids Res. 2004 32: D383-D387; doi:10.1093/nar/gkh001 [Abstract] [FREE Full Text] [Print PDF]  

Setsuko Komatsu, Keiichi Kojima, Kouji Suzuki, Kazuo Ozaki, and Kenichi Higo

Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003
Nucl. Acids Res. 2004 32: D388-D392; doi:10.1093/nar/gkh020 [Abstract] [FREE Full Text] [Print PDF]  

Carolyn J. Lawrence, Qunfeng Dong, Mary L. Polacco, Trent E. Seigfried, and Volker Brendel

MaizeGDB, the community database for maize genetics and genomics
Nucl. Acids Res. 2004 32: D393-D397; doi:10.1093/nar/gkh011 [Abstract] [FREE Full Text] [Print PDF]  

Nadim W. Alkharouf and Benjamin F. Matthews

SGMD: the Soybean Genomics and Microarray Database
Nucl. Acids Res. 2004 32: D398-D400; doi:10.1093/nar/gkh126 [Abstract] [FREE Full Text] [Print PDF]  

J. E. Mabey, M. J. Anderson, P. F. Giles, C. J. Miller, T. K. Attwood, N. W. Paton, E. Bornberg-Bauer, G. D. Robson, S. G. Oliver, and D. W. Denning

CADRE: the Central Aspergillus Data REpository
Nucl. Acids Res. 2004 32: D401-D405; doi:10.1093/nar/gkh009 [Abstract] [FREE Full Text] [Print PDF]  

Kristin C. Gunsalus, Wan-Chen Yueh, Philip MacMenamin, and Fabio Piano

RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects
Nucl. Acids Res. 2004 32: D406-D410; doi:10.1093/nar/gkh110 [Abstract] [FREE Full Text] [Print PDF]  

Todd W. Harris, Nansheng Chen, Fiona Cunningham, Marcela Tello-Ruiz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Muller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz, Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth, Paul W. Sternberg, and Lincoln D. Stein

WormBase: a multi-species resource for nematode biology and genomics
Nucl. Acids Res. 2004 32: D411-D417; doi:10.1093/nar/gkh066 [Abstract] [FREE Full Text] [Print PDF]  

Reed J. Kelso, Michael Buszczak, Ana T. Quiñones, Claudia Castiblanco, Stacy Mazzalupo, and Lynn Cooley

Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster
Nucl. Acids Res. 2004 32: D418-D420; doi:10.1093/nar/gkh014 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Jagan Srinivasan, Georg W. Otto, Ulrich Kahlow, Robert Geisler, and Ralf J. Sommer

AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus
Nucl. Acids Res. 2004 32: D421-D422; doi:10.1093/nar/gkh057 [Abstract] [FREE Full Text] [Print PDF]  

Todd Wylie, John C. Martin, Michael Dante, Makedonka Dautova Mitreva, Sandra W. Clifton, Asif Chinwalla, Robert H. Waterston, Richard K. Wilson, and James P. McCarter

Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
Nucl. Acids Res. 2004 32: D423-D426; doi:10.1093/nar/gkh010 [Abstract] [FREE Full Text] [Print PDF]  

John Parkinson, Claire Whitton, Ralf Schmid, Marian Thomson, and Mark Blaxter

NEMBASE: a resource for parasitic nematode ESTs
Nucl. Acids Res. 2004 32: D427-D430; doi:10.1093/nar/gkh018 [Abstract] [FREE Full Text] [Print PDF]  

Ida Schomburg, Antje Chang, Christian Ebeling, Marion Gremse, Christian Heldt, Gregor Huhn, and Dietmar Schomburg

BRENDA, the enzyme database: updates and major new developments
Nucl. Acids Res. 2004 32: D431-D433; doi:10.1093/nar/gkh081 [Abstract] [FREE Full Text] [Print PDF]  

Astrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Wolfgang Fleischmann, Sinéad Boyce, Kristian B. Axelsen, Amos Bairoch, Dietmar Schomburg, Keith F. Tipton, and Rolf Apweiler

IntEnz, the integrated relational enzyme database
Nucl. Acids Res. 2004 32: D434-D437; doi:10.1093/nar/gkh119 [Abstract] [FREE Full Text] [Print PDF]  

Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, Alfred Wang, Suzanne Paley, Martha Arnaud, John Pick, Seung Y. Rhee, and Peter D. Karp

MetaCyc: a multiorganism database of metabolic pathways and enzymes
Nucl. Acids Res. 2004 32: D438-D442; doi:10.1093/nar/gkh100 [Abstract] [FREE Full Text] [Print PDF]  

Christian Lemer, Erick Antezana, Fabian Couche, Frédéric Fays, Xavier Santolaria, Rekin’s Janky, Yves Deville, Jean Richelle, and Shoshana J. Wodak

The aMAZE LightBench: a web interface to a relational database of cellular processes
Nucl. Acids Res. 2004 32: D443-D448; doi:10.1093/nar/gkh139 [Abstract] [FREE Full Text] [Print PDF]  

Lukasz Salwinski, Christopher S. Miller, Adam J. Smith, Frank K. Pettit, James U. Bowie, and David Eisenberg

The Database of Interacting Proteins: 2004 update
Nucl. Acids Res. 2004 32: D449-D451; doi:10.1093/nar/gkh086 [Abstract] [FREE Full Text] [Print PDF]  

Henning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David Sherman, and Rolf Apweiler

IntAct: an open source molecular interaction database
Nucl. Acids Res. 2004 32: D452-D455; doi:10.1093/nar/gkh052 [Abstract] [FREE Full Text] [Print PDF]  

Ming Chen, Susana Lin, and Ralf Hofestaedt

STCDB: Signal Transduction Classification Database
Nucl. Acids Res. 2004 32: D456-D458; doi:10.1093/nar/gkh079 [Abstract] [FREE Full Text] [Print PDF]  

C. Andreoli, H. Prokisch, K. Hörtnagel, J. C. Mueller, M. Münsterkötter, C. Scharfe, and T. Meitinger

MitoP2, an integrated database on mitochondrial proteins in yeast and man
Nucl. Acids Res. 2004 32: D459-D462; doi:10.1093/nar/gkh137 [Abstract] [FREE Full Text] [Print PDF]  

Dawn Cotter, Purnima Guda, Eoin Fahy, and Shankar Subramaniam

MitoProteome: mitochondrial protein sequence database and annotation system
Nucl. Acids Res. 2004 32: D463-D467; doi:10.1093/nar/gkh048 [Abstract] [FREE Full Text] [Print PDF]  

E. Birney, D. Andrews, P. Bevan, M. Caccamo, G. Cameron, Y. Chen, L. Clarke, G. Coates, T. Cox, J. Cuff, V. Curwen, T. Cutts, T. Down, R. Durbin, E. Eyras, X. M. Fernandez-Suarez, P. Gane, B. Gibbins, J. Gilbert, M. Hammond, H. Hotz, V. Iyer, A. Kahari, K. Jekosch, A. Kasprzyk, D. Keefe, S. Keenan, H. Lehvaslaiho, G. McVicker, C. Melsopp, P. Meidl, E. Mongin, R. Pettett, S. Potter, G. Proctor, M. Rae, S. Searle, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, A. Ureta-Vidal, C. Woodwark, M. Clamp, and T. Hubbard

Ensembl 2004
Nucl. Acids Res. 2004 32: D468-D470; doi:10.1093/nar/gkh038 [Abstract] [FREE Full Text] [Print PDF]  

Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, RIKEN GER Group, GSL Members, Akihiko Konagaya, and Christian Schönbach

FREP: a database of functional repeats in mouse cDNAs
Nucl. Acids Res. 2004 32: D471-D475; doi:10.1093/nar/gkh123 [Abstract] [FREE Full Text] [Print PDF]  

Carol J. Bult, Judith A. Blake, Joel E. Richardson, James A. Kadin, Janan T. Eppig, and the Mouse Genome Database Group

The Mouse Genome Database (MGD): integrating biology with the genome
Nucl. Acids Res. 2004 32: D476-D481; doi:10.1093/nar/gkh125 [Abstract] [FREE Full Text] [Print PDF]  

Petr Divina and Jirí Forejt

The Mouse SAGE Site: database of public mouse SAGE libraries
Nucl. Acids Res. 2004 32: D482-D483; doi:10.1093/nar/gkh058 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Hirohide Uenishi, Tomoko Eguchi, Kohei Suzuki, Tetsuya Sawazaki, Daisuke Toki, Hiroki Shinkai, Naohiko Okumura, Noriyuki Hamasima, and Takashi Awata

PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries
Nucl. Acids Res. 2004 32: D484-D488; doi:10.1093/nar/gkh037 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Tal Dagan, Rotem Sorek, Eilon Sharon, Gil Ast, and Dan Graur

AluGene: a database of Alu elements incorporated within protein-coding genes
Nucl. Acids Res. 2004 32: D489-D492; doi:10.1093/nar/gkh132 [Abstract] [FREE Full Text] [Print PDF]  

Donna Karolchik, Angela S. Hinrichs, Terrence S. Furey, Krishna M. Roskin, Charles W. Sugnet, David Haussler, and W. James Kent

The UCSC Table Browser data retrieval tool
Nucl. Acids Res. 2004 32: D493-D496; doi:10.1093/nar/gkh103 [Abstract] [FREE Full Text] [Print PDF]  

Suraj Peri, J. Daniel Navarro, Troels Z. Kristiansen, Ramars Amanchy, Vineeth Surendranath, Babylakshmi Muthusamy, T. K. B. Gandhi, K. N. Chandrika, Nandan Deshpande, Shubha Suresh, B. P. Rashmi, K. Shanker, N. Padma, Vidya Niranjan, H. C. Harsha, Naveen Talreja, B. M. Vrushabendra, M. A. Ramya, A. J. Yatish, Mary Joy, H. N. Shivashankar, M. P. Kavitha, Minal Menezes, Dipanwita Roy Choudhury, Neelanjana Ghosh, R. Saravana, Sreenath Chandran, Sujatha Mohan, Chandra Kiran Jonnalagadda, C. K. Prasad, Chandan Kumar-Sinha, Krishna S. Deshpande, and Akhilesh Pandey

Human protein reference database as a discovery resource for proteomics
Nucl. Acids Res. 2004 32: D497-D501; doi:10.1093/nar/gkh070 [Abstract] [FREE Full Text] [Print PDF]  

Reiko Kikuno, Takahiro Nagase, Manabu Nakayama, Hisashi Koga, Noriko Okazaki, Daisuke Nakajima, and Osamu Ohara

HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE
Nucl. Acids Res. 2004 32: D502-D504; doi:10.1093/nar/gkh035 [Abstract] [FREE Full Text] [Print PDF]  

Detlev Bannasch, Alexander Mehrle, Karl-Heinz Glatting, Rainer Pepperkok, Annemarie Poustka, and Stefan Wiemann

LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system
Nucl. Acids Res. 2004 32: D505-D508; doi:10.1093/nar/gkh022 [Abstract] [FREE Full Text] [Print PDF]  

Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, and C. Victor Jongeneel

trome, trEST and trGEN: databases of predicted protein sequences
Nucl. Acids Res. 2004 32: D509-D511; doi:10.1093/nar/gkh067 [Abstract] [FREE Full Text] [Print PDF]  

Paul N. Schofield, Jonathan B. L. Bard, Catherine Booth, Jacques Boniver, Vincenzo Covelli, Philippe Delvenne, Michele Ellender, Wilhelm Engstrom, Wolfgang Goessner, Michael Gruenberger, Heinz Hoefler, John Hopewell, Mariatheresa Mancuso, Carmel Mothersill, Christopher S. Potten, Leticia Quintanilla-Fend, Bjorn Rozell, Hannu Sariola, John P. Sundberg, and Andrew Ward

Pathbase: a database of mutant mouse pathology
Nucl. Acids Res. 2004 32: D512-D515; doi:10.1093/nar/gkh124 [Abstract] [FREE Full Text] [Print PDF]  

D. Fredman, G. Munns, D. Rios, F. Sjöholm, M. Siegfried, B. Lenhard, H. Lehväslaiho, and A. J. Brookes

HGVbase: a curated resource describing human DNA variation and phenotype relationships
Nucl. Acids Res. 2004 32: D516-D519; doi:10.1093/nar/gkh111 [Abstract] [FREE Full Text] [Print PDF]  

Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Simon Kasif, and Jie Liang

topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
Nucl. Acids Res. 2004 32: D520-D522; doi:10.1093/nar/gkh104 [Abstract] [FREE Full Text] [Print PDF]  

Keiko Akagi, Takeshi Suzuki, Robert M. Stephens, Nancy A. Jenkins, and Neal G. Copeland

RTCGD: retroviral tagged cancer gene database
Nucl. Acids Res. 2004 32: D523-D527; doi:10.1093/nar/gkh013 [Abstract] [FREE Full Text] [Print PDF]  

Bernice R. Packer, Meredith Yeager, Brian Staats, Robert Welch, Andrew Crenshaw, Maureen Kiley, Andrew Eckert, Michael Beerman, Edward Miller, Andrew Bergen, Nathaniel Rothman, Robert Strausberg, and Stephen J. Chanock

SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes
Nucl. Acids Res. 2004 32: D528-D532; doi:10.1093/nar/gkh005 [Abstract] [FREE Full Text] [Print PDF]  

Suisheng Tang, Hao Han, and Vladimir B. Bajic

ERGDB: Estrogen Responsive Genes Database
Nucl. Acids Res. 2004 32: D533-D536; doi:10.1093/nar/gkh083 [Abstract] [FREE Full Text] [Print PDF]  

George P. Patrinos, Belinda Giardine, Cathy Riemer, Webb Miller, David H. K. Chui, Nicholas P. Anagnou, Henri Wajcman, and Ross C. Hardison

Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies
Nucl. Acids Res. 2004 32: D537-D541; doi:10.1093/nar/gkh006 [Abstract] [FREE Full Text] [Print PDF]  

Viviane Praz, Vidhya Jagannathan, and Philipp Bucher

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature
Nucl. Acids Res. 2004 32: D542-D547; doi:10.1093/nar/gkh107 [Abstract] [FREE Full Text] [Print PDF]  

Itoshi Nikaido, Chika Saito, Akiko Wakamoto, Yasuhiro Tomaru, Takahiro Arakawa, Yoshihide Hayashizaki, and Yasushi Okazaki

EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes
Nucl. Acids Res. 2004 32: D548-D551; doi:10.1093/nar/gkh093 [Abstract] [FREE Full Text] [Print PDF]  

Axel Visel, Christina Thaller, and Gregor Eichele

GenePaint.org: an atlas of gene expression patterns in the mouse embryo
Nucl. Acids Res. 2004 32: D552-D556; doi:10.1093/nar/gkh029 [Abstract] [FREE Full Text] [Print PDF]  

Christine To, Trevor Epp, Tammy Reid, Qing Lan, Mei Yu, Carol Y. J. Li, Minako Ohishi, Paula Hant, Nora Tsao, Guillermo Casallo, Janet Rossant, Lucy R. Osborne, and William L. Stanford

The Centre for Modeling Human Disease Gene Trap resource
Nucl. Acids Res. 2004 32: D557-D559; doi:10.1093/nar/gkh106 [Abstract] [FREE Full Text] [Print PDF]  

C. Wiederkehr, R. Basavaraj, C. Sarrauste de Menthière, L. Hermida, R. Koch, U. Schlecht, A. Amon, S. Brachat, M. Breitenbach, P. Briza, S. Caburet, M. Cherry, R. Davis, A. Deutschbauer, H. G. Dickinson, T. Dumitrescu, M. Fellous, A. Goldman, J. A. Grootegoed, R. Hawley, R. Ishii, B. Jégou, R. J. Kaufman, F. Klein, N. Lamb, B. Maro, K. Nasmyth, A. Nicolas, T. Orr-Weaver, P. Philippsen, C. Pineau, K. P. Rabitsch, V. Reinke, H. Roest, W. Saunders, M. Schröder, T. Schedl, M. Siep, A. Villeneuve, D. J. Wolgemuth, M. Yamamoto, D. Zickler, R. E. Esposito, and M. Primig

GermOnline, a cross-species community knowledgebase on germ cell differentiation
Nucl. Acids Res. 2004 32: D560-D567; doi:10.1093/nar/gkh055 [Abstract] [FREE Full Text] [Print PDF]  

David P. Hill, Dale A. Begley, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Constance M. Smith, Jon S. Beal, Lori E. Corbani, Judith A. Blake, Janan T. Eppig, James A. Kadin, Joel E. Richardson, and Martin Ringwald

The mouse Gene Expression Database (GXD): updates and enhancements
Nucl. Acids Res. 2004 32: D568-D571; doi:10.1093/nar/gkh069 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Sung-Ho Goh, Y. Terry Lee, Gerard G. Bouffard, and Jeffery L. Miller

Hembase: browser and genome portal for hematology and erythroid biology
Nucl. Acids Res. 2004 32: D572-D574; doi:10.1093/nar/gkh129 [Abstract] [FREE Full Text] [Print PDF]  

David J. Craigon, Nick James, John Okyere, Janet Higgins, Joan Jotham, and Sean May

NASCArrays: a repository for microarray data generated by NASC’s transcriptomics service
Nucl. Acids Res. 2004 32: D575-D577; doi:10.1093/nar/gkh133 [Abstract] [FREE Full Text] [Print PDF]  

Josephine Chen, Po Zhao, Donald Massaro, Linda B. Clerch, Richard R. Almon, Debra C. DuBois, William J. Jusko, and Eric P. Hoffman

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface
Nucl. Acids Res. 2004 32: D578-D581; doi:10.1093/nar/gkh003 [Abstract] [FREE Full Text] [Print PDF]  

György Babnigg and Carol S. Giometti

GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes
Nucl. Acids Res. 2004 32: D582-D585; doi:10.1093/nar/gkh089 [Abstract] [FREE Full Text] [Print PDF]  

M. Brahmachary, S. P. T. Krishnan, J. L. Y. Koh, A. M. Khan, S. H. Seah, T. W. Tan, V. Brusic, and V. B. Bajic

ANTIMIC: a database of antimicrobial sequences
Nucl. Acids Res. 2004 32: D586-D589; doi:10.1093/nar/gkh032 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material]  

Zhe Wang and Guangshun Wang

APD: the Antimicrobial Peptide Database
Nucl. Acids Res. 2004 32: D590-D592; doi:10.1093/nar/gkh025 [Abstract] [FREE Full Text] [Print PDF]  

Lee Whitmore and B. A. Wallace

The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols
Nucl. Acids Res. 2004 32: D593-D594; doi:10.1093/nar/gkh077 [Abstract] [FREE Full Text] [Print PDF]  

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Feng Liang, Udayakumar Matrubutham, Babak Parvizi, Jessica Yen, Daniel Duan, Jyotika Mirchandani, Sandra Hashima, Uyen Nguyen, Eric Ubil, Jake Loewenheim, Xin Yu, Sara Sipes, Wendy Williams, Ling Wang, Robert Bennett, and John Carrino

ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection
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