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 Contents: Volume 33, Database Issue    January 1 2005    [Index by Author] 
       Editorial
       Articles
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Editorial:

Alex Bateman
Editorial
Nucl. Acids Res. 2005 33: D1; doi:10.1093/nar/gki133 [FREE Full Text]   OPEN ACCESS ARTICLE  

Dov Greenbaum, Andrew Smith, and Mark Gerstein
Editorial
Nucl. Acids Res. 2005 33: D3-D4; doi:10.1093/nar/gki134 [FREE Full Text]   OPEN ACCESS ARTICLE  

Articles:

Michael Y. Galperin
The Molecular Biology Database Collection: 2005 update
Nucl. Acids Res. 2005 33: D5-D24; doi:10.1093/nar/gki139 [Abstract] [FREE Full Text] [Database Summaries]   OPEN ACCESS ARTICLE  

Y. Tateno, N. Saitou, K. Okubo, H. Sugawara, and T. Gojobori
DDBJ in collaboration with mass-sequencing teams on annotation
Nucl. Acids Res. 2005 33: D25-D28; doi:10.1093/nar/gki020 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Carola Kanz, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Alastair Baldwin, Kirsty Bates, Paul Browne, Alexandra van den Broek, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Federico Garcia Diez, Nicola Harte, Tamara Kulikova, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Siamak Sobhany, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler
The EMBL Nucleotide Sequence Database
Nucl. Acids Res. 2005 33: D29-D33; doi:10.1093/nar/gki098 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
GenBank
Nucl. Acids Res. 2005 33: D34-D38; doi:10.1093/nar/gki063 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Wolfgang Helmberg, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Joan U. Pontius, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Grigory Starchenko, Tugba O. Suzek, Roman Tatusov, Tatiana A. Tatusova, Lukas Wagner, and Eugene Yaschenko
Database resources of the National Center for Biotechnology Information
Nucl. Acids Res. 2005 33: D39-D45; doi:10.1093/nar/gki062 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Catherine Brooksbank, Graham Cameron, and Janet Thornton
The European Bioinformatics Institute's data resources: towards systems biology
Nucl. Acids Res. 2005 33: D46-D53; doi:10.1093/nar/gki026 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Donna Maglott, Jim Ostell, Kim D. Pruitt, and Tatiana Tatusova
Entrez Gene: gene-centered information at NCBI
Nucl. Acids Res. 2005 33: D54-D58; doi:10.1093/nar/gki031 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Khelifi Adel, Duret Laurent, and Mouchiroud Dominique
HOPPSIGEN: a database of human and mouse processed pseudogenes
Nucl. Acids Res. 2005 33: D59-D66; doi:10.1093/nar/gki084 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Victor G. Levitsky, Aleksey V. Katokhin, Olga A. Podkolodnaya, Dagmara P. Furman, and Nikolay A. Kolchanov
NPRD: Nucleosome Positioning Region Database
Nucl. Acids Res. 2005 33: D67-D70; doi:10.1093/nar/gki049 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Y. Lee, J. Tsai, S. Sunkara, S. Karamycheva, G. Pertea, R. Sultana, V. Antonescu, A. Chan, F. Cheung, and J. Quackenbush
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes
Nucl. Acids Res. 2005 33: D71-D74; doi:10.1093/nar/gki064 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Pora Kim, Namshin Kim, Younghee Lee, Bumjin Kim, Youngah Shin, and Sanghyuk Lee
ECgene: genome annotation for alternative splicing
Nucl. Acids Res. 2005 33: D75-D79; doi:10.1093/nar/gki118 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Hsien-Da Huang, Jorng-Tzong Horng, Feng-Mao Lin, Yu-Chung Chang, and Chen-Chia Huang
SpliceInfo: an information repository for mRNA alternative splicing in human genome
Nucl. Acids Res. 2005 33: D80-D85; doi:10.1093/nar/gki129 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Endre Barta, Endre Sebestyén, Tamás B. Pálfy, Gábor Tóth, Csaba P. Ortutay, and László Patthy
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
Nucl. Acids Res. 2005 33: D86-D90; doi:10.1093/nar/gki097 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Voichita D. Marinescu, Isaac S. Kohane, and Alberto Riva
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites
Nucl. Acids Res. 2005 33: D91-D97; doi:10.1093/nar/gki103 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Abel D. González, Vladimir Espinosa, Ana T. Vasconcelos, Ernesto Pérez-Rueda, and Julio Collado-Vides
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes
Nucl. Acids Res. 2005 33: D98-D102; doi:10.1093/nar/gki054 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Fang Zhao, Zhenyu Xuan, Lihua Liu, and Michael Q. Zhang
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies
Nucl. Acids Res. 2005 33: D103-D107; doi:10.1093/nar/gki004 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Matthias Truss, Maciej Swat, Szymon M. Kielbasa, Reinhold Schäfer, Hanspeter Herzel, and Christian Hagemeier
HuSiDa—the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells
Nucl. Acids Res. 2005 33: D108-D111; doi:10.1093/nar/gki131 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Changning Liu, Baoyan Bai, Geir Skogerbř, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, and Runsheng Chen
NONCODE: an integrated knowledge database of non-coding RNAs
Nucl. Acids Res. 2005 33: D112-D115; doi:10.1093/nar/gki041 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Haibo Zhang, Jun Hu, Michael Recce, and Bin Tian
PolyA_DB: a database for mammalian mRNA polyadenylation
Nucl. Acids Res. 2005 33: D116-D120; doi:10.1093/nar/gki055 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, and Alex Bateman
Rfam: annotating non-coding RNAs in complete genomes
Nucl. Acids Res. 2005 33: D121-D124; doi:10.1093/nar/gki081 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Ken C. Pang, Stuart Stephen, Pär G. Engström, Khairina Tajul-Arifin, Weisan Chen, Claes Wahlestedt, Boris Lenhard, Yoshihide Hayashizaki, and John S. Mattick
RNAdb—a comprehensive mammalian noncoding RNA database
Nucl. Acids Res. 2005 33: D125-D130; doi:10.1093/nar/gki089 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, and Erik L. L. Sonnhammer
siRNAdb: a database of siRNA sequences
Nucl. Acids Res. 2005 33: D131-D134; doi:10.1093/nar/gki136 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

James A. McCloskey and Jef Rozenski
The Small Subunit rRNA Modification Database
Nucl. Acids Res. 2005 33: D135-D138; doi:10.1093/nar/gki015 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Mathias Sprinzl and Konstantin S. Vassilenko
Compilation of tRNA sequences and sequences of tRNA genes
Nucl. Acids Res. 2005 33: D139-D140; doi:10.1093/nar/gki012 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Flavio Mignone, Giorgio Grillo, Flavio Licciulli, Michele Iacono, Sabino Liuni, Paul J. Kersey, Jorge Duarte, Cecilia Saccone, and Graziano Pesole
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
Nucl. Acids Res. 2005 33: D141-D146; doi:10.1093/nar/gki021 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, and Nicholas Lamb
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
Nucl. Acids Res. 2005 33: D147-D153; doi:10.1093/nar/gki120 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Amos Bairoch, Rolf Apweiler, 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
The Universal Protein Resource (UniProt)
Nucl. Acids Res. 2005 33: D154-D159; doi:10.1093/nar/gki070 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Sven Mika and Burkhard Rost
NMPdb: Database of Nuclear Matrix Proteins
Nucl. Acids Res. 2005 33: D160-D163; doi:10.1093/nar/gki132 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Sébastien Rey, Michael Acab, Jennifer L. Gardy, Matthew R. Laird, Katalin deFays, Christophe Lambert, and Fiona S. L. Brinkman
PSORTdb: a protein subcellular localization database for bacteria
Nucl. Acids Res. 2005 33: D164-D168; doi:10.1093/nar/gki027 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Yunjia Chen, Yong Zhang, Yanbin Yin, Ge Gao, Songgang Li, Ying Jiang, Xiaocheng Gu, and Jingchu Luo
SPD—a web-based secreted protein database
Nucl. Acids Res. 2005 33: D169-D173; doi:10.1093/nar/gki093 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Ya-Hui Chang, Wen-Hui Su, Tso-Ching Lee, Hsiao-Fang Sunny Sun, Chia-Hsiang Chen, Wen-Harn Pan, Shih-Feng Tsai, and Yuh-Shan Jou
TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations
Nucl. Acids Res. 2005 33: D174-D177; doi:10.1093/nar/gki102 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Qiaojuan Jane Su, Lin Lu, Serge Saxonov, and Douglas L. Brutlag
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity
Nucl. Acids Res. 2005 33: D178-D182; doi:10.1093/nar/gki060 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Vladimir A. Ivanisenko, Sergey S. Pintus, Dmitry A. Grigorovich, and Nickolay A. Kolchanov
PDBSite: a database of the 3D structure of protein functional sites
Nucl. Acids Res. 2005 33: D183-D187; doi:10.1093/nar/gki105 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Andreas Heger, Christopher Andrew Wilton, Ashwin Sivakumar, and Liisa Holm
ADDA: a domain database with global coverage of the protein universe
Nucl. Acids Res. 2005 33: D188-D191; doi:10.1093/nar/gki096 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Aron Marchler-Bauer, John B. Anderson, Praveen F. Cherukuri, Carol DeWeese-Scott, Lewis Y. Geer, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, and Stephen H. Bryant
CDD: a Conserved Domain Database for protein classification
Nucl. Acids Res. 2005 33: D192-D196; doi:10.1093/nar/gki069 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Saraswathi Abhiman and Erik L. L. Sonnhammer
FunShift: a database of function shift analysis on protein subfamilies
Nucl. Acids Res. 2005 33: D197-D200; doi:10.1093/nar/gki067 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex Mitchell, Anastasia N. Nikolskaya, Sandra Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, and Cathy H. Wu
InterPro, progress and status in 2005
Nucl. Acids Res. 2005 33: D201-D205; doi:10.1093/nar/gki106 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Shu-Hsien Sheu, David R. Lancia, Jr, Karl H. Clodfelter, Melissa R. Landon, and Sandor Vajda
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes
Nucl. Acids Res. 2005 33: D206-D211; doi:10.1093/nar/gki091 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Catherine Bru, Emmanuel Courcelle, Sébastien Carrčre, Yoann Beausse, Sandrine Dalmar, and Daniel Kahn
The ProDom database of protein domain families: more emphasis on 3D
Nucl. Acids Res. 2005 33: D212-D215; doi:10.1093/nar/gki034 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Noam Kaplan, Ori Sasson, Uri Inbar, Moriah Friedlich, Menachem Fromer, Hillel Fleischer, Elon Portugaly, Nathan Linial, and Michal Linial
ProtoNet 4.0: A hierarchical classification of one million protein sequences
Nucl. Acids Res. 2005 33: D216-D218; doi:10.1093/nar/gki007 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

James Casbon and Mansoor A. S. Saqi
S4: structure-based sequence alignments of SCOP superfamilies
Nucl. Acids Res. 2005 33: D219-D222; doi:10.1093/nar/gki043 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Kristian Vlahovicek, László Kaján, Vilmos Ágoston, and Sándor Pongor
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines
Nucl. Acids Res. 2005 33: D223-D225; doi:10.1093/nar/gki112 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Thomas Meinel, Antje Krause, Hannes Luz, Martin Vingron, and Eike Staub
The SYSTERS Protein Family Database in 2005
Nucl. Acids Res. 2005 33: D226-D229; doi:10.1093/nar/gki030 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis
REBASE—restriction enzymes and DNA methyltransferases
Nucl. Acids Res. 2005 33: D230-D232; doi:10.1093/nar/gki029 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Nita Deshpande, Kenneth J. Addess, Wolfgang F. Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John Westbrook, Helen M. Berman, and Philip E. Bourne
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema
Nucl. Acids Res. 2005 33: D233-D237; doi:10.1093/nar/gki057 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Jae-Min Shin and Doo-Ho Cho
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures
Nucl. Acids Res. 2005 33: D238-D241; doi:10.1093/nar/gki059 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Thomas Lütteke, Martin Frank, and Claus-W. von der Lieth
Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB
Nucl. Acids Res. 2005 33: D242-D246; doi:10.1093/nar/gki013 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Frances Pearl, Annabel Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony Lewis, Christopher Bennett, Russell Marsden, Alistair Grant, David Lee, Adrian Akpor, Michael Maibaum, Andrew Harrison, Timothy Dallman, Gabrielle Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline Johnston, Antonio Sillero, Janet Thornton, and Christine Orengo
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
Nucl. Acids Res. 2005 33: D247-D251; doi:10.1093/nar/gki024 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Ganesan Pugalenthi, Anirban Bhaduri, and Ramanathan Sowdhamini
GenDiS: Genomic Distribution of protein structural domain Superfamilies
Nucl. Acids Res. 2005 33: D252-D255; doi:10.1093/nar/gki087 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Véronique Giudicelli, Denys Chaume, and Marie-Paule Lefranc
IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes
Nucl. Acids Res. 2005 33: D256-D261; doi:10.1093/nar/gki010 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

S. Velankar, P. McNeil, V. Mittard-Runte, A. Suarez, D. Barrell, R. Apweiler, and K. Henrick
E-MSD: an integrated data resource for bioinformatics
Nucl. Acids Res. 2005 33: D262-D265; doi:10.1093/nar/gki058 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Roman A. Laskowski, Victor V. Chistyakov, and Janet M. Thornton
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids
Nucl. Acids Res. 2005 33: D266-D268; doi:10.1093/nar/gki001 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Goran Neshich, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Ivan P. Pinto, Juliana F. Palandrani, Joăo N. Krauchenco, Christian Baudet, Arnaldo J. Montagner, and Roberto H. Higa
STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database
Nucl. Acids Res. 2005 33: D269-D274; doi:10.1093/nar/gki111 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Gábor E. Tusnády, Zsuzsanna Dosztányi, and István Simon
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank
Nucl. Acids Res. 2005 33: D275-D278; doi:10.1093/nar/gki002 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Kate F. Fulton, Glyn L. Devlin, Rachel A. Jodun, Linda Silvestri, Stephen P. Bottomley, Alan R. Fersht, and Ashley M. Buckle
PFD: a database for the investigation of protein folding kinetics and stability
Nucl. Acids Res. 2005 33: D279-D283; doi:10.1093/nar/gki016 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano, and Paul D. Thomas
The PANTHER database of protein families, subfamilies, functions and pathways
Nucl. Acids Res. 2005 33: D284-D288; doi:10.1093/nar/gki078 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, and Russ B. Altman
Biomedical term mapping databases
Nucl. Acids Res. 2005 33: D289-D293; doi:10.1093/nar/gki137 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

J. R. Cole, B. Chai, R. J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, G. M. Garrity, and J. M. Tiedje
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
Nucl. Acids Res. 2005 33: D294-D296; doi:10.1093/nar/gki038 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Paul Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, Alexander Kanapin, Ujjwal Das, Karine Michoud, Isabelle Phan, Alexandre Gattiker, Tamara Kulikova, Nadeem Faruque, Karyn Duggan, Peter Mclaren, Britt Reimholz, Laurent Duret, Simon Penel, Ingmar Reuter, and Rolf Apweiler
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
Nucl. Acids Res. 2005 33: D297-D302; doi:10.1093/nar/gki039 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

José M. Peregrín-Alvarez, Andrew Yam, Gaya Sivakumar, and John Parkinson
PartiGeneDB—collating partial genomes
Nucl. Acids Res. 2005 33: D303-D307; doi:10.1093/nar/gki109 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

M. Louise Riley, Thorsten Schmidt, Christian Wagner, Hans-Werner Mewes, and Dmitrij Frishman
The PEDANT genome database in 2005
Nucl. Acids Res. 2005 33: D308-D310; doi:10.1093/nar/gki019 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Elliot J. Lefkowitz, Chris Upton, Shankar S. Changayil, Charles Buck, Paula Traktman, and R. Mark L. Buller
Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource
Nucl. Acids Res. 2005 33: D311-D316; doi:10.1093/nar/gki110 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Paul Stothard, Gary Van Domselaar, Savita Shrivastava, Anchi Guo, Brian O'Neill, Joseph Cruz, Michael Ellison, and David S. Wishart
BacMap: an interactive picture atlas of annotated bacterial genomes
Nucl. Acids Res. 2005 33: D317-D320; doi:10.1093/nar/gki075 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Hiroyuki Ogata and Jean-Michel Claverie
Metagrowth: a new resource for the building of metabolic hypotheses in microbiology
Nucl. Acids Res. 2005 33: D321-D324; doi:10.1093/nar/gki042 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, and Qi Jin
VFDB: a reference database for bacterial virulence factors
Nucl. Acids Res. 2005 33: D325-D328; doi:10.1093/nar/gki008 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Raju V. Misra, Richard S. P. Horler, Wolfgang Reindl, Igor I. Goryanin, and Gavin H. Thomas
EchoBASE: an integrated post-genomic database for Escherichia coli
Nucl. Acids Res. 2005 33: D329-D333; doi:10.1093/nar/gki028 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne Paley, Ian T. Paulsen, Martín Peralta-Gil, and Peter D. Karp
EcoCyc: a comprehensive database resource for Escherichia coli
Nucl. Acids Res. 2005 33: D334-D337; doi:10.1093/nar/gki108 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Geoffrey L. Winsor, Raymond Lo, Shannan J. Ho Sui, Korine S.E. Ung, Shaoshan Huang, Dean Cheng, Wai-Kay Ho Ching, Robert E. W. Hancock, and Fiona S. L. Brinkman
Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation
Nucl. Acids Res. 2005 33: D338-D343; doi:10.1093/nar/gki047 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy, K. R. Rajyashri, Villoo Morawala Patell, and Chris Bowler
The Diatom EST Database
Nucl. Acids Res. 2005 33: D344-D347; doi:10.1093/nar/gki121 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Leandro Hermida, Sophie Brachat, Sylvia Voegeli, Peter Philippsen, and Michael Primig
The Ashbya Genome Database (AGD)—a tool for the yeast community and genome biologists
Nucl. Acids Res. 2005 33: D348-D352; doi:10.1093/nar/gki009 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

C. d'Enfert, S. Goyard, S. Rodriguez-Arnaveilhe, L. Frangeul, L. Jones, F. Tekaia, O. Bader, Antje Albrecht, L. Castillo, A. Dominguez, J. F. Ernst, C. Fradin, C. Gaillardin, S. Garcia-Sanchez, P. de Groot, B. Hube, F. M. Klis, S. Krishnamurthy, D. Kunze, M.-C. Lopez, A. Mavor, N. Martin, I. Moszer, D. Onésime, J. Perez Martin, R. Sentandreu, E. Valentin, and A. J. P. Brown
CandidaDB: a genome database for Candida albicans pathogenomics
Nucl. Acids Res. 2005 33: D353-D357; doi:10.1093/nar/gki124 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Gail Binkley, Christopher Lane, Stuart R. Miyasato, and Gavin Sherlock
The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information
Nucl. Acids Res. 2005 33: D358-D363; doi:10.1093/nar/gki003 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

U. Güldener, M. Münsterkötter, G. Kastenmüller, N. Strack, J. van Helden, C. Lemer, J. Richelles, S. J. Wodak, J. García-Martínez, J. E. Pérez-Ortín, H. Michael, A. Kaps, E. Talla, B. Dujon, B. André, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, and H. W. Mewes
CYGD: the Comprehensive Yeast Genome Database
Nucl. Acids Res. 2005 33: D364-D368; doi:10.1093/nar/gki053 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Ilona Pylvänäinen, Graham J. L. Kemp, Olle Nerman, and Anders Blomberg
PROPHECY—a database for high-resolution phenomics
Nucl. Acids Res. 2005 33: D369-D373; doi:10.1093/nar/gki126 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert Nash, Rose Oughtred, Marek Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Anand Sethuraman, Shuai Weng, David Botstein, and J. Michael Cherry
Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)
Nucl. Acids Res. 2005 33: D374-D377; doi:10.1093/nar/gki023 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Michael Riffle, Lars Malmström, and Trisha N. Davis
The Yeast Resource Center Public Data Repository
Nucl. Acids Res. 2005 33: D378-D382; doi:10.1093/nar/gki073 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Nansheng Chen, Todd W. Harris, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Payan Canaran, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Fiona Cunningham, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Muller, Cecilia Nakamura, Shraddha Pai, 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 comprehensive data resource for Caenorhabditis biology and genomics
Nucl. Acids Res. 2005 33: D383-D389; doi:10.1093/nar/gki066 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Rachel A. Drysdale, Madeline A. Crosby, and The FlyBase Consortium
FlyBase: genes and gene models
Nucl. Acids Res. 2005 33: D390-D395; doi:10.1093/nar/gki046 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Andre R. O. Cavalcanti, Thomas H. Clarke, and Laura F. Landweber
MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates
Nucl. Acids Res. 2005 33: D396-D398; doi:10.1093/nar/gki130 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, Guo Yu, Haifeng Yuan, Yafeng Hu, Ruiqiang Li, Tao Feng, Chen Ye, Cheng Lu, Jun Wang, Songgang Li, Gane Ka-Shu Wong, Huanming Yang, Jian Wang, Zhonghuai Xiang, Zeyang Zhou, and Jun Yu
SilkDB: a knowledgebase for silkworm biology and genomics
Nucl. Acids Res. 2005 33: D399-D402; doi:10.1093/nar/gki116 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

M. D. Prasad, M. Muthulakshmi, K. P. Arunkumar, M. Madhu, V. B. Sreenu, V. Pavithra, B. Bose, H. A. Nagarajaram, K. Mita, T. Shimada, and J. Nagaraju
SilkSatDb: a microsatellite database of the silkworm, Bombyx mori
Nucl. Acids Res. 2005 33: D403-D406; doi:10.1093/nar/gki099 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Nozomi Nagano
EzCatDB: the Enzyme Catalytic-mechanism Database
Nucl. Acids Res. 2005 33: D407-D412; doi:10.1093/nar/gki080 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Amelie Stein, Robert B. Russell, and Patrick Aloy
3did: interacting protein domains of known three-dimensional structure
Nucl. Acids Res. 2005 33: D413-D417; doi:10.1093/nar/gki037 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, M. Bajec, K. Bantoft, D. Betel, B. Bobechko, K. Boutilier, E. Burgess, K. Buzadzija, R. Cavero, C. D'Abreo, I. Donaldson, D. Dorairajoo, M. J. Dumontier, M. R. Dumontier, V. Earles, R. Farrall, H. Feldman, E. Garderman, Y. Gong, R. Gonzaga, V. Grytsan, E. Gryz, V. Gu, E. Haldorsen, A. Halupa, R. Haw, A. Hrvojic, L. Hurrell, R. Isserlin, F. Jack, F. Juma, A. Khan, T. Kon, S. Konopinsky, V. Le, E. Lee, S. Ling, M. Magidin, J. Moniakis, J. Montojo, S. Moore, B. Muskat, I. Ng, J. P. Paraiso, B. Parker, G. Pintilie, R. Pirone, J. J. Salama, S. Sgro, T. Shan, Y. Shu, J. Siew, D. Skinner, K. Snyder, R. Stasiuk, D. Strumpf, B. Tuekam, S. Tao, Z. Wang, M. White, R. Willis, C. Wolting, S. Wong, A. Wrong, C. Xin, R. Yao, B. Yates, S. Zhang, K. Zheng, T. Pawson, B. F. F. Ouellette, and C. W. V. Hogue
The Biomolecular Interaction Network Database and related tools 2005 update
Nucl. Acids Res. 2005 33: D418-D424; doi:10.1093/nar/gki051 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

E. A. Ananko, N. L. Podkolodny, I. L. Stepanenko, O. A. Podkolodnaya, D. A. Rasskazov, D. S. Miginsky, V. A. Likhoshvai, A. V. Ratushny, N. N. Podkolodnaya, and N. A. Kolchanov
GeneNet in 2005
Nucl. Acids Res. 2005 33: D425-D427; doi:10.1093/nar/gki077 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

G. Joshi-Tope, M. Gillespie, I. Vastrik, P. D'Eustachio, E. Schmidt, B. de Bono, B. Jassal, G.R. Gopinath, G.R. Wu, L. Matthews, S. Lewis, E. Birney, and L. Stein
Reactome: a knowledgebase of biological pathways
Nucl. Acids Res. 2005 33: D428-D432; doi:10.1093/nar/gki072 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Christian von Mering, Lars J. Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, and Peer Bork
STRING: known and predicted protein–protein associations, integrated and transferred across organisms
Nucl. Acids Res. 2005 33: D433-D437; doi:10.1093/nar/gki005 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Jing Wang, Ximiao He, Jue Ruan, Mingtao Dai, Jie Chen, Yong Zhang, Yafeng Hu, Chen Ye, Shengting Li, Lijuan Cong, Lin Fang, Bin Liu, Songgang Li, Jian Wang, David W. Burt, Gane Ka-Shu Wong, Jun Yu, Huanming Yang, and Jun Wang
ChickVD: a sequence variation database for the chicken genome
Nucl. Acids Res. 2005 33: D438-D441; doi:10.1093/nar/gki092 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Vamsi Veeramachaneni and Wojciech Makalowski
DED: Database of Evolutionary Distances
Nucl. Acids Res. 2005 33: D442-D446; doi:10.1093/nar/gki094 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark, and E. Birney
Ensembl 2005
Nucl. Acids Res. 2005 33: D447-D453; doi:10.1093/nar/gki138 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, and W. James Kent
The UCSC Proteome Browser
Nucl. Acids Res. 2005 33: D454-D458; doi:10.1093/nar/gki100 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, P. Meidl, S. M. Searle, J. Stalker, R. Storey, S. Trevanion, L. Wilming, and T. Hubbard
The Vertebrate Genome Annotation (Vega) database
Nucl. Acids Res. 2005 33: D459-D465; doi:10.1093/nar/gki135 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Laura Elnitski, Belinda Giardine, Prachi Shah, Yi Zhang, Cathy Riemer, Matthew Weirauch, Richard Burhans, Webb Miller, and Ross C. Hardison
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results
Nucl. Acids Res. 2005 33: D466-D470; doi:10.1093/nar/gki045 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, and the Mouse Genome Database Group
The Mouse Genome Database (MGD): from genes to mice—a community resource for mouse biology
Nucl. Acids Res. 2005 33: D471-D475; doi:10.1093/nar/gki113 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Kevin P. O'Brien, Maido Remm, and Erik L. L. Sonnhammer
Inparanoid: a comprehensive database of eukaryotic orthologs
Nucl. Acids Res. 2005 33: D476-D480; doi:10.1093/nar/gki107 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Eric Bazin, Laurent Duret, Simon Penel, and Nicolas Galtier
Polymorphix: a sequence polymorphism database
Nucl. Acids Res. 2005 33: D481-D484; doi:10.1093/nar/gki076 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Norberto de la Cruz, Susan Bromberg, Dean Pasko, Mary Shimoyama, Simon Twigger, Jiali Chen, Chin-Fu Chen, Chunyu Fan, Cindy Foote, Gopal R. Gopinath, Glenn Harris, Aubrey Hughes, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Natalya Nenasheva, Jeff Nie, Rajni Nigam, Victoria Petri, Dorothy Reilly, Weiye Wang, Wenhua Wu, Angela Zuniga-Meyer, Lan Zhao, Anne Kwitek, Peter Tonellato, and Howard Jacob
The Rat Genome Database (RGD): developments towards a phenome database
Nucl. Acids Res. 2005 33: D485-D491; doi:10.1093/nar/gki050 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Greta Petersen, Per Johnson, Lars Andersson, Karin Klinga-Levan, Pedro M. Gómez-Fabre, and Fredrik Stĺhl
RatMap—rat genome tools and data
Nucl. Acids Res. 2005 33: D492-D494; doi:10.1093/nar/gki125 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Christian Roth, Matthew J. Betts, Pär Steffansson, Gisle Sćlensminde, and David A. Liberles
The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics
Nucl. Acids Res. 2005 33: D495-D497; doi:10.1093/nar/gki090 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Tobias Penzkofer, Thomas Dandekar, and Tomasz Zemojtel
L1Base: from functional annotation to prediction of active LINE-1 elements
Nucl. Acids Res. 2005 33: D498-D500; doi:10.1093/nar/gki044 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Kim D. Pruitt, Tatiana Tatusova, and Donna R. Maglott
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
Nucl. Acids Res. 2005 33: D501-D504; doi:10.1093/nar/gki025 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, and Sandro Banfi
DG-CST (Disease Gene Conserved Sequence Tags), a database of human–mouse conserved elements associated to disease genes
Nucl. Acids Res. 2005 33: D505-D510; doi:10.1093/nar/gki011 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Robert Hoffmann, Joaquin Dopazo, Juan C. Cigudosa, and Alfonso Valencia
HCAD, closing the gap between breakpoints and genes
Nucl. Acids Res. 2005 33: D511-D513; doi:10.1093/nar/gki061 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Ada Hamosh, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, and Victor A. McKusick
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
Nucl. Acids Res. 2005 33: D514-D517; doi:10.1093/nar/gki033 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Hyo Jin Kang, Kyoung Oak Choi, Byung-Dong Kim, Sangsoo Kim, and Young Joo Kim
FESD: a Functional Element SNPs Database in human
Nucl. Acids Res. 2005 33: D518-D522; doi:10.1093/nar/gki082 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

James Robinson, Matthew J. Waller, Peter Stoehr, and Steven G. E. Marsh
IPD—the Immuno Polymorphism Database
Nucl. Acids Res. 2005 33: D523-D526; doi:10.1093/nar/gki032 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Joke Reumers, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Francois Stricher, Luis Serrano, and Frederic Rousseau
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs
Nucl. Acids Res. 2005 33: D527-D532; doi:10.1093/nar/gki086 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, and Kenta Nakai
Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues
Nucl. Acids Res. 2005 33: D533-D536; doi:10.1093/nar/gki117 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Joăo Pedro de Magalhăes, Joana Costa, and Olivier Toussaint
HAGR: the Human Ageing Genomic Resources
Nucl. Acids Res. 2005 33: D537-D543; doi:10.1093/nar/gki017 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Luc J. Smink, Erin M. Helton, Barry C. Healy, Christopher C. Cavnor, Alex C. Lam, Daisy Flamez, Oliver S. Burren, Yang Wang, Geoffrey E. Dolman, David B. Burdick, Vincent H. Everett, Gustavo Glusman, Davide Laneri, Lee Rowen, Helen Schuilenburg, Neil M. Walker, Josyf Mychaleckyj, Linda S. Wicker, Decio L. Eizirik, John A. Todd, and Nathan Goodman
T1DBase, a community web-based resource for type 1 diabetes research
Nucl. Acids Res. 2005 33: D544-D549; doi:10.1093/nar/gki095 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Yasuhiro Kasai, Shin-ichi Hashimoto, Tomoyuki Yamada, Jun Sese, Sumio Sugano, Kouji Matsushima, and Shinichi Morishita
5'SAGE: 5'-end Serial Analysis of Gene Expression database
Nucl. Acids Res. 2005 33: D550-D552; doi:10.1093/nar/gki085 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

H. Parkinson, U. Sarkans, M. Shojatalab, N. Abeygunawardena, S. Contrino, R. Coulson, A. Farne, G. Garcia Lara, E. Holloway, M. Kapushesky, P. Lilja, G. Mukherjee, A. Oezcimen, T. Rayner, P. Rocca-Serra, A. Sharma, S. Sansone, and A. Brazma
ArrayExpress—a public repository for microarray gene expression data at the EBI
Nucl. Acids Res. 2005 33: D553-D555; doi:10.1093/nar/gki056 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Maxim Shklar, Liora Strichman-Almashanu, Orit Shmueli, Michael Shmoish, Marilyn Safran, and Doron Lancet
GeneTide—Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases
Nucl. Acids Res. 2005 33: D556-D561; doi:10.1093/nar/gki122 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Tanya Barrett, Tugba O. Suzek, Dennis B. Troup, Stephen E. Wilhite, Wing-Chi Ngau, Pierre Ledoux, Dmitry Rudnev, Alex E. Lash, Wataru Fujibuchi, and Ron Edgar
NCBI GEO: mining millions of expression profiles—database and tools
Nucl. Acids Res. 2005 33: D562-D566; doi:10.1093/nar/gki022 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Motohiko Tanino, Marie-Anne Debily, Takuro Tamura, Teruyoshi Hishiki, Osamu Ogasawara, Katsuji Murakawa, Shoko Kawamoto, Kouichi Itoh, Shinya Watanabe, Sandro José de Souza, Sandrine Imbeaud, Esther Graudens, Eric Eveno, Phillip Hilton, Yukio Sudo, Janet Kelso, Kazuho Ikeo, Tadashi Imanishi, Takashi Gojobori, Charles Auffray, Winston Hide, and Kousaku Okubo
The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms
Nucl. Acids Res. 2005 33: D567-D572; doi:10.1093/nar/gki104 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Vishal Shah, Sriram Sridhar, Jennifer Beane, Jerome S. Brody, and Avrum Spira
SIEGE: Smoking Induced Epithelial Gene Expression Database
Nucl. Acids Res. 2005 33: D573-D579; doi:10.1093/nar/gki035 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Catherine A. Ball, Ihab A. B. Awad, Janos Demeter, Jeremy Gollub, Joan M. Hebert, Tina Hernandez-Boussard, Heng Jin, John C. Matese, Michael Nitzberg, Farrell Wymore, Zachariah K. Zachariah, Patrick O. Brown, and Gavin Sherlock
The Stanford Microarray Database accommodates additional microarray platforms and data formats
Nucl. Acids Res. 2005 33: D580-D582; doi:10.1093/nar/gki006 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Oliver Drews and Angelika Görg
DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels
Nucl. Acids Res. 2005 33: D583-D587; doi:10.1093/nar/gki101 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Florencio Pazos, David Guijas, Alfonso Valencia, and Victor De Lorenzo
MetaRouter: bioinformatics for bioremediation
Nucl. Acids Res. 2005 33: D588-D592; doi:10.1093/nar/gki068 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Marie-Paule Lefranc, Véronique Giudicelli, Quentin Kaas, Elodie Duprat, Joumana Jabado-Michaloud, Dominique Scaviner, Chantal Ginestoux, Oliver Clément, Denys Chaume, and Gérard Lefranc
IMGT, the international ImMunoGeneTics information system®
Nucl. Acids Res. 2005 33: D593-D597; doi:10.1093/nar/gki065 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Nuwee Wiwatwattana and Anuj Kumar
Organelle DB: a cross-species database of protein localization and function
Nucl. Acids Res. 2005 33: D598-D604; doi:10.1093/nar/gki071 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Joshua L. Heazlewood and A. Harvey Millar
AMPDB: the Arabidopsis Mitochondrial Protein Database
Nucl. Acids Res. 2005 33: D605-D610; doi:10.1093/nar/gki048 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Marty C. Brandon, Marie T. Lott, Kevin Cuong Nguyen, Syawal Spolim, Shamkant B. Navathe, Pierre Baldi, and Douglas C. Wallace
MITOMAP: a human mitochondrial genome database—2004 update
Nucl. Acids Res. 2005 33: D611-D613; doi:10.1093/nar/gki079 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, and Julie A. Dickerson
BarleyBase—an expression profiling database for plant genomics
Nucl. Acids Res. 2005 33: D614-D618; doi:10.1093/nar/gki123 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

C. Künne, M. Lange, T. Funke, H. Miehe, T. Thiel, I. Grosse, and U. Scholz
CR-EST: a resource for crop ESTs
Nucl. Acids Res. 2005 33: D619-D621; doi:10.1093/nar/gki119 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

Stephen Rudd
openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections
Nucl. Acids Res. 2005 33: D622-D627; doi:10.1093/nar/gki040 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Stephen Rudd, Heiko Schoof, and Klaus Mayer
PlantMarkers—a database of predicted molecular markers from plants
Nucl. Acids Res. 2005 33: D628-D632; doi:10.1093/nar/gki074 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

John W. S. Brown, Peter J. Shaw, Paul Shaw, and David F. Marshall
Arabidopsis nucleolar protein database (AtNoPDB)
Nucl. Acids Res. 2005 33: D633-D636; doi:10.1093/nar/gki052 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Adam M. Gustafson, Edwards Allen, Scott Givan, Daniel Smith, James C. Carrington, and Kristin D. Kasschau
ASRP: the Arabidopsis Small RNA Project Database
Nucl. Acids Res. 2005 33: D637-D640; doi:10.1093/nar/gki127 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Sébastien Aubourg, Véronique Brunaud, Clémence Bruyčre, Mark Cock, Richard Cooke, Annick Cottet, Arnaud Couloux, Patrice Déhais, Gilbert Deléage, Aymeric Duclert, Manuel Echeverria, Aimée Eschbach, Denis Falconet, Ghislain Filippi, Christine Gaspin, Christophe Geourjon, Jean-Michel Grienenberger, Guy Houlné, Elisabeth Jamet, Frédéric Lechauve, Olivier Leleu, Philippe Leroy, Régis Mache, Christian Meyer, Hafed Nedjari, Ioan Negrutiu, Valérie Orsini, Eric Peyretaillade, Cyril Pommier, Jeroen Raes, Jean-Loup Risler, Stéphane Rivičre, Stéphane Rombauts, Pierre Rouzé, Michel Schneider, Philippe Schwob, Ian Small, Ghislain Soumayet-Kampetenga, Darko Stankovski, Claire Toffano, Michael Tognolli, Michel Caboche, and Alain Lecharny
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts
Nucl. Acids Res. 2005 33: D641-D646; doi:10.1093/nar/gki115 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Motoaki Seki, Takashi Kuromori, Takuya Ito, Akihiko Konagaya, Tetsuro Toyoda, and Kazuo Shinozaki
RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome
Nucl. Acids Res. 2005 33: D647-D650; doi:10.1093/nar/gki014 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Yuichi Ito, Kohji Arikawa, Baltazar A. Antonio, Isamu Ohta, Shinji Naito, Yoshiyuki Mukai, Atsuko Shimano, Masatoshi Masukawa, Michie Shibata, Mayu Yamamoto, Yukiyo Ito, Junri Yokoyama, Yasumichi Sakai, Katsumi Sakata, Yoshiaki Nagamura, Nobukazu Namiki, Takashi Matsumoto, Kenichi Higo, and Takuji Sasaki
Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics
Nucl. Acids Res. 2005 33: D651-D655; doi:10.1093/nar/gki083 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Christopher G. Love, Andrew J. Robinson, Geraldine A. C. Lim, Clare J. Hopkins, Jacqueline Batley, Gary Barker, German C. Spangenberg, and David Edwards
Brassica ASTRA: an integrated database for Brassica genomic research
Nucl. Acids Res. 2005 33: D656-D659; doi:10.1093/nar/gki036 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Michael D. Gonzales, Eric Archuleta, Andrew Farmer, Kamal Gajendran, David Grant, Randy Shoemaker, William D. Beavis, and Mark E. Waugh
The Legume Information System (LIS): an integrated information resource for comparative legume biology
Nucl. Acids Res. 2005 33: D660-D665; doi:10.1093/nar/gki128 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Svenja Meyer, Axel Nagel, and Christiane Gebhardt
PoMaMo—a comprehensive database for potato genome data
Nucl. Acids Res. 2005 33: D666-D670; doi:10.1093/nar/gki018 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Ida Retter, Hans Helmar Althaus, Richard Münch, and Werner Müller
VBASE2, an integrative V gene database
Nucl. Acids Res. 2005 33: D671-D674; doi:10.1093/nar/gki088 [Abstract] [FREE Full Text]   OPEN ACCESS ARTICLE  

Susie M. Stephens, Jake Y. Chen, Marcel G. Davidson, Shiby Thomas, and Barry M. Trute
Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences
Nucl. Acids Res. 2005 33: D675-D679; doi:10.1093/nar/gki114 [Abstract] [FREE Full Text] [Supplementary Material]   OPEN ACCESS ARTICLE  

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