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Previous Next 		Contents: Volume 35, Database issue    January 2007    [Index by Author] 
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Editorial:Back

Alex Batemen
EDITORIAL
Nucl. Acids Res. 2007 35: D1-D2; doi:10.1093/nar/gkl1051 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:Back

Michael Y. Galperin
The Molecular Biology Database Collection: 2007 update
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D3-D4; doi:10.1093/nar/gkl1008 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Database Summaries] [Request Permissions]  

David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Vadim Miller, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, and Eugene Yaschenko
Database resources of the National Center for Biotechnology Information
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D5-D12; doi:10.1093/nar/gkl1031 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hideaki Sugawara, Takashi Abe, Takashi Gojobori, and Yoshio Tateno
DDBJ working on evaluation and classification of bacterial genes in INSDC
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D13-D15; doi:10.1093/nar/gkl908 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tamara Kulikova, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Lawrence Bower, Paul Browne, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Carola Kanz, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Sheila Plaister, Siamak Sobhany, Peter Stoehr, Robert Vaughan, Dan Wu, Weimin Zhu, and Rolf Apweiler
EMBL Nucleotide Sequence Database in 2006
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D16-D20; doi:10.1093/nar/gkl913 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler
GenBank
Nucl. Acids Res. 2007 35: D21-D25; doi:10.1093/nar/gkl986 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Donna Maglott, Jim Ostell, Kim D. Pruitt, and Tatiana Tatusova
Entrez Gene: gene-centered information at NCBI
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D26-D31; doi:10.1093/nar/gkl993 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

C. Dieterich, M. W. Franz, and M. Vingron
Developments in CORG: a gene-centric comparative genomics resource
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D32-D35; doi:10.1093/nar/gkl977 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sunil Archak, Eshwar Meduri, P. Sravana Kumar, and J. Nagaraju
InSatDb: a microsatellite database of fully sequenced insect genomes
Nucleic Acids Research Advance Access published on November 1, 2006
Nucl. Acids Res. 2007 35: D36-D39; doi:10.1093/nar/gkl778 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Conrad A. Nieduszynski, Shin-ichiro Hiraga, Prashanth Ak, Craig J. Benham, and Anne D. Donaldson
OriDB: a DNA replication origin database
Nucleic Acids Research Advance Access published on October 25, 2006
Nucl. Acids Res. 2007 35: D40-D46; doi:10.1093/nar/gkl758 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Byungwook Lee, Taehyung Kim, Seon-Kyu Kim, Kwang H. Lee, and Doheon Lee
Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications
Nucleic Acids Research Advance Access published on November 3, 2006
Nucl. Acids Res. 2007 35: D47-D50; doi:10.1093/nar/gkl807 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lei Bao, Mi Zhou, Ligang Wu, Lu Lu, Dan Goldowitz, Robert W. Williams, and Yan Cui
PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D51-D54; doi:10.1093/nar/gkl797 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul Harrrison, and Mark Gerstein
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D55-D60; doi:10.1093/nar/gkl851 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kim D. Pruitt, Tatiana Tatusova, and Donna R. Maglott
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D61-D65; doi:10.1093/nar/gkl842 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cristian Chaparro, Romain Guyot, Andrea Zuccolo, Benoît Piégu, and Olivier Panaud
RetrOryza: a database of the rice LTR-retrotransposons
Nucleic Acids Research Advance Access published on October 28, 2006
Nucl. Acids Res. 2007 35: D66-D70; doi:10.1093/nar/gkl780 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

I. Agrafioti and M. P. H. Stumpf
SNPSTR: a database of compound microsatellite-SNP markers
Nucl. Acids Res. 2007 35: D71-D75; doi:10.1093/nar/gkl806 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gang Wu, Yuanpu Zheng, Imran Qureshi, Htar Thant Zin, Tyler Beck, Blazej Bulka, and Stephen J. Freeland
SGDB: a database of synthetic genes re-designed for optimizing protein over-expression
Nucleic Acids Research Advance Access published on October 24, 2006
Nucl. Acids Res. 2007 35: D76-D79; doi:10.1093/nar/gkl648 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yevgeniy Gelfand, Alfredo Rodriguez, and Gary Benson
TRDB—The Tandem Repeats Database
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D80-D87; doi:10.1093/nar/gkl1013 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Axel Visel, Simon Minovitsky, Inna Dubchak, and Len A. Pennacchio
VISTA Enhancer Browser—a database of tissue-specific human enhancers
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D88-D92; doi:10.1093/nar/gkl822 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Namshin Kim, Alexander V. Alekseyenko, Meenakshi Roy, and Christopher Lee
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D93-D98; doi:10.1093/nar/gkl884 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yeunsook Lee, Younghee Lee, Bumjin Kim, Youngah Shin, Seungyoon Nam, Pora Kim, Namshin Kim, Won-Hyong Chung, Jaesang Kim, and Sanghyuk Lee
ECgene: an alternative splicing database update
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D99-D103; doi:10.1093/nar/gkl992 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, and Tadashi Imanishi
H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D104-D109; doi:10.1093/nar/gkl854 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tyler S. Alioto
U12DB: a database of orthologous U12-type spliceosomal introns
Nucleic Acids Research Advance Access published on November 1, 2006
Nucl. Acids Res. 2007 35: D110-D115; doi:10.1093/nar/gkl796 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anil G. Jegga, Jing Chen, Sivakumar Gowrisankar, Mrunal A. Deshmukh, RangaChandra Gudivada, Sue Kong, Vivek Kaimal, and Bruce J. Aronow
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
Nucleic Acids Research Advance Access published on December 18, 2006
Nucl. Acids Res. 2007 35: D116-D121; doi:10.1093/nar/gkl1011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Vincent Ferretti, Christian Poitras, Dominique Bergeron, Benoit Coulombe, François Robert, and Mathieu Blanchette
PReMod: a database of genome-wide mammalian cis-regulatory module predictions
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D122-D126; doi:10.1093/nar/gkl879 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mikhail Pachkov, Ionas Erb, Nacho Molina, and Erik van Nimwegen
SwissRegulon: a database of genome-wide annotations of regulatory sites
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D127-D131; doi:10.1093/nar/gkl857 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Abel González Pérez, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, and Julio Collado-Vides
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D132-D136; doi:10.1093/nar/gkl800 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

C. Jiang, Z. Xuan, F. Zhao, and M. Q. Zhang
TRED: a transcriptional regulatory element database, new entries and other development
Nucl. Acids Res. 2007 35: D137-D140; doi:10.1093/nar/gkl1041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tao He, Pufeng Du, and Yanda Li
dbRES: a web-oriented database for annotated RNA editing sites
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D141-D144; doi:10.1093/nar/gkl815 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, and Kiyoshi Asai
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D145-D148; doi:10.1093/nar/gkl837 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Molly Megraw, Praveen Sethupathy, Benoit Corda, and Artemis G. Hatzigeorgiou
miRGen: a database for the study of animal microRNA genomic organization and function
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D149-D155; doi:10.1093/nar/gkl904 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yong Zhang, Jiongtang Li, Lei Kong, Ge Gao, Qing-Rong Liu, and Liping Wei
NATsDB: Natural Antisense Transcripts DataBase
Nucleic Acids Research Advance Access published on November 1, 2006
Nucl. Acids Res. 2007 35: D156-D161; doi:10.1093/nar/gkl782 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maciej Szymanski, Volker A. Erdmann, and Jan Barciszewski
Noncoding RNAs database (ncRNAdb)
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D162-D164; doi:10.1093/nar/gkl994 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ju Youn Lee, Ijen Yeh, Ji Yeon Park, and Bin Tian
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes
Nucl. Acids Res. 2007 35: D165-D168; doi:10.1093/nar/gkl870 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. R. Cole, B. Chai, R. J. Farris, Q. Wang, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, A. M. Bandela, E. Cardenas, G. M. Garrity, and J. M. Tiedje
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D169-D172; doi:10.1093/nar/gkl889 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ernesto Picardi, Teresa Maria Rosaria Regina, Axel Brennicke, and Carla Quagliariello
REDIdb: the RNA editing database
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D173-D177; doi:10.1093/nar/gkl793 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ken C. Pang, Stuart Stephen, Marcel E. Dinger, Pär G. Engström, Boris Lenhard, and John S. Mattick
RNAdb 2.0—an expanded database of mammalian non-coding RNAs
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D178-D182; doi:10.1093/nar/gkl926 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jun Xie, Ming Zhang, Tao Zhou, Xia Hua, LiSha Tang, and Weilin Wu
Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D183-D187; doi:10.1093/nar/gkl873 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael Hiller, Swetlana Nikolajewa, Klaus Huse, Karol Szafranski, Philip Rosenstiel, Stefan Schuster, Rolf Backofen, and Matthias Platzer
TassDB: a database of alternative tandem splice sites
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D188-D192; doi:10.1093/nar/gkl762 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

The UniProt Consortium
The Universal Protein Resource (UniProt)
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D193-D197; doi:10.1093/nar/gkl929 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen, and Michael K. Gilson
BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D198-D201; doi:10.1093/nar/gkl999 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Di Wu, Feng Cui, Robert Jernigan, and Zhijun Wu
PIDD: database for Protein Inter-atomic Distance Distributions
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D202-D207; doi:10.1093/nar/gkl802 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andea Pierleoni, Pier Luigi Martelli, Piero Fariselli, and Rita Casadio
eSLDB: eukaryotic subcellular localization database
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D208-D212; doi:10.1093/nar/gkl775 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Joshua L. Heazlewood, Robert E. Verboom, Julian Tonti-Filippini, Ian Small, and A. Harvey Millar
SUBA: the Arabidopsis Subcellular Database
Nucleic Acids Research Advance Access published on October 28, 2006
Nucl. Acids Res. 2007 35: D213-D218; doi:10.1093/nar/gkl863 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gonzalo Lopez, A. Valencia, and M. Tress
FireDB—a database of functionally important residues from proteins of known structure
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D219-D223; doi:10.1093/nar/gkl897 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Virginie Buillard, Lorenzo Cerutti, Richard Copley, Emmanuel Courcelle, Ujjwal Das, Louise Daugherty, Mark Dibley, Robert Finn, Wolfgang Fleischmann, Julian Gough, Daniel Haft, Nicolas Hulo, Sarah Hunter, Daniel Kahn, Alexander Kanapin, Anish Kejariwal, Alberto Labarga, Petra S. Langendijk-Genevaux, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Anastasia N. Nikolskaya, Sandra Orchard, Christine Orengo, Robert Petryszak, Jeremy D. Selengut, Christian J. A. Sigrist, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, and Corin Yeats
New developments in the InterPro database
Nucl. Acids Res. 2007 35: D224-D228; doi:10.1093/nar/gkl841 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, and Manuela Helmer-Citterich
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D229-D231; doi:10.1093/nar/gkl922 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paolo Sonego, Mircea Pacurar, Somdutta Dhir, Attila Kertész-Farkas, András Kocsor, Zoltán Gáspári, Jack A.M. Leunissen, and Sándor Pongor
A Protein Classification Benchmark collection for machine learning
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D232-D236; doi:10.1093/nar/gkl812 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Aron Marchler-Bauer, John B. Anderson, Myra K. Derbyshire, Carol DeWeese-Scott, Noreen R. Gonzales, Marc Gwadz, Luning Hao, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Dmitri Krylov, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H. Marchler, Mikhail Mullokandov, James S. Song, Narmada Thanki, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, and Stephen H. Bryant
CDD: a conserved domain database for interactive domain family analysis
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D237-D240; doi:10.1093/nar/gkl951 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Elon Portugaly, Nathan Linial, and Michal Linial
EVEREST: a collection of evolutionary conserved protein domains
Nucleic Acids Research Advance Access published on November 11, 2006
Nucl. Acids Res. 2007 35: D241-D246; doi:10.1093/nar/gkl850 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Huaiyu Mi, Nan Guo, Anish Kejariwal, and Paul D. Thomas
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D247-D252; doi:10.1093/nar/gkl869 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Antonina Andreeva, Andreas Prlic, Tim J. P. Hubbard, and Alexey G. Murzin
SISYPHUS—structural alignments for proteins with non-trivial relationships
Nucleic Acids Research Advance Access published on October 26, 2006
Nucl. Acids Res. 2007 35: D253-D259; doi:10.1093/nar/gkl746 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Jeremy D. Selengut, Daniel H. Haft, Tanja Davidsen, Anurhada Ganapathy, Michelle Gwinn-Giglio, William C. Nelson, Alexander R. Richter, and Owen White
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D260-D264; doi:10.1093/nar/gkl1043 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shalin Seebah, Anita Suresh, Shaowei Zhuo, Yong How Choong, Hazel Chua, Danny Chuon, Roger Beuerman, and Chandra Verma
Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D265-D268; doi:10.1093/nar/gkl866 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Richard J. Roberts, Tamas Vincze, Janos Posfai, and Dana Macelis
REBASE—enzymes and genes for DNA restriction and modification
Nucl. Acids Res. 2007 35: D269-D270; doi:10.1093/nar/gkl891 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mark D'Souza, Elizabeth M. Glass, Mustafa H. Syed, Yi Zhang, Alexis Rodriguez, Natalia Maltsev, and Michael Y. Galperin
Sentra: a database of signal transduction proteins for comparative genome analysis
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D271-D273; doi:10.1093/nar/gkl949 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Qinghu Ren, Kaixi Chen, and Ian T. Paulsen
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D274-D279; doi:10.1093/nar/gkl925 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Philip Toukach, Hiren J Joshi, René Ranzinger, Yuri Knirel, and Claus-W. von der Lieth
Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de
Nucl. Acids Res. 2007 35: D280-D286; doi:10.1093/nar/gkl883 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Frank, T. Lütteke, and C.-W. von der Lieth
GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages
Nucl. Acids Res. 2007 35: 287-290; doi:10.1093/nar/gkl907 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lesley H. Greene, Tony E. Lewis, Sarah Addou, Alison Cuff, Tim Dallman, Mark Dibley, Oliver Redfern, Frances Pearl, Rekha Nambudiry, Adam Reid, Ian Sillitoe, Corin Yeats, Janet M. Thornton, and Christine A. Orengo
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D291-D297; doi:10.1093/nar/gkl959 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yanli Wang, Kenneth J. Addess, Jie Chen, Lewis Y. Geer, Jane He, Siqian He, Shennan Lu, Thomas Madej, Aron Marchler-Bauer, Paul A. Thiessen, Naigong Zhang, and Stephen H. Bryant
MMDB: annotating protein sequences with Entrez's 3D-structure database
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D298-D300; doi:10.1093/nar/gkl952 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Helen Berman, Kim Henrick, Haruki Nakamura, and John L. Markley
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D301-D303; doi:10.1093/nar/gkl971 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kate F. Fulton, Mark A. Bate, Noel G. Faux, Khalid Mahmood, Chris Betts, and Ashley M. Buckle
Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D304-D307; doi:10.1093/nar/gkl1007 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Derek Wilson, Martin Madera, Christine Vogel, Cyrus Chothia, and Julian Gough
The SUPERFAMILY database in 2007: families and functions
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D308-D313; doi:10.1093/nar/gkl910 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Michael Gromiha, Yukimitsu Yabuki, Srinesh Kundu, Sivasundaram Suharnan, and Makiko Suwa
TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D314-D316; doi:10.1093/nar/gkl805 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chesley M. Leslin, Alexej Abyzov, and Valentin A. Ilyin
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method
Nucleic Acids Research Advance Access published on October 25, 2006
Nucl. Acids Res. 2007 35: D317-D321; doi:10.1093/nar/gkl809 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gil Alterovitz, Michael Xiang, Mamta Mohan, and Marco F. Ramoni
GO PaD: the Gene Ontology Partition Database
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D322-D327; doi:10.1093/nar/gkl799 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data] [Request Permissions]  

Yuying Tian and Allan W. Dickerman
GeneTrees: a phylogenomics resource for prokaryotes
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D328-D331; doi:10.1093/nar/gkl905 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

T. Ryan Gregory, James A. Nicol, Heidi Tamm, Bellis Kullman, Kaur Kullman, Ilia J. Leitch, Brian G. Murray, Donald F. Kapraun, Johann Greilhuber, and Michael D. Bennett
Eukaryotic genome size databases
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D332-D338; doi:10.1093/nar/gkl828 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Masaki Hirahata, Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, and Hideaki Sugawara
Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes
Nucleic Acids Research Advance Access published on December 7, 2006
Nucl. Acids Res. 2007 35: D339-D342; doi:10.1093/nar/gkl1004 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ikuo Uchiyama
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups
Nucleic Acids Research Advance Access published on November 29, 2006
Nucl. Acids Res. 2007 35: D343-D346; doi:10.1093/nar/gkl978 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz, Daniela Bartels, Matthew Cohoon, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Kaitlyn Hwang, Michael Kubal, Gohar Rem Margaryan, Folker Meyer, William Mihalo, Gary J. Olsen, Robert Olson, Andrei Osterman, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D. Pusch, Dmitry A. Rodionov, Xinghua Shi, Olga Vassieva, Veronika Vonstein, Olga Zagnitko, Fangfang Xia, Jenifer Zinner, Ross Overbeek, and Rick Stevens
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
Nucleic Acids Research Advance Access published on December 1, 2006
Nucl. Acids Res. 2007 35: D347-D353; doi:10.1093/nar/gkl947 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Louise Riley, Thorsten Schmidt, Irena I. Artamonova, Christian Wagner, Andreas Volz, Klaus Heumann, Hans-Werner Mewes, and Dmitrij Frishman
PEDANT genome database: 10 years online
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D354-D357; doi:10.1093/nar/gkl1005 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christian von Mering, Lars J. Jensen, Michael Kuhn, Samuel Chaffron, Tobias Doerks, Beate Krüger, Berend Snel, and Peer Bork
STRING 7—recent developments in the integration and prediction of protein interactions
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D358-D362; doi:10.1093/nar/gkl825 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christophe Combet, Nicolas Garnier, Céline Charavay, Delphine Grando, Daniel Crisan, Julien Lopez, Alexandre Dehne-Garcia, Christophe Geourjon, Emmanuel Bettler, Chantal Hulo, Philippe Le Mercier, Ralf Bartenschlager, Helmut Diepolder, Darius Moradpour, Jean-Michel Pawlotsky, Charles M. Rice, Christian Trépo, François Penin, and Gilbert Deléage
euHCVdb: the European hepatitis C virus database
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D363-D366; doi:10.1093/nar/gkl970 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Saravanamuttu Gnaneshan, Samreen Ijaz, Joanne Moran, Mary Ramsay, and Jonathan Green
HepSEQ: International Public Health Repository for Hepatitis B
Nucleic Acids Research Advance Access published on November 27, 2006
Nucl. Acids Res. 2007 35: D367-D370; doi:10.1093/nar/gkl874 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Calvin Pan, Joseph Kim, Lamei Chen, Qi Wang, and Christopher Lee
The HIV positive selection mutation database
Nucleic Acids Research Advance Access published on November 15, 2006
Nucl. Acids Res. 2007 35: D371-D375; doi:10.1093/nar/gkl855 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Suhua Chang, Jiajie Zhang, Xiaoyun Liao, Xinxing Zhu, Dahai Wang, Jiang Zhu, Tao Feng, Baoli Zhu, George F. Gao, Jian Wang, Huanming Yang, Jun Yu, and Jing Wang
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research
Nucleic Acids Research Advance Access published on October 25, 2006
Nucl. Acids Res. 2007 35: D376-D380; doi:10.1093/nar/gkl779 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paul Wei-Che Hsu, Li-Zen Lin, Sheng-Da Hsu, Justin Bo-Kai Hsu, and Hsien-Da Huang
ViTa: prediction of host microRNAs targets on viruses
Nucleic Acids Research Advance Access published on December 5, 2006
Nucl. Acids Res. 2007 35: D381-D385; doi:10.1093/nar/gkl1009 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Luke E. Ulrich and Igor B. Zhulin
MiST: a microbial signal transduction database
Nucleic Acids Research Advance Access published on November 28, 2006
Nucl. Acids Res. 2007 35: D386-D390; doi:10.1093/nar/gkl932 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

C. E. Zhou, J. Smith, M. Lam, A. Zemla, M. D. Dyer, and T. Slezak
MvirDB—a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D391-D394; doi:10.1093/nar/gkl791 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sung Ho Yoon, Young-Kyu Park, Soohyun Lee, Doil Choi, Tae Kwang Oh, Cheol-Goo Hur, and Jihyun F. Kim
Towards pathogenomics: a web-based resource for pathogenicity islands
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D395-D400; doi:10.1093/nar/gkl790 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

E. E. Snyder, N. Kampanya, J. Lu, E. K. Nordberg, H. R. Karur, M. Shukla, J. Soneja, Y. Tian, T. Xue, H. Yoo, F. Zhang, C. Dharmanolla, N. V. Dongre, J. J. Gillespie, J. Hamelius, M. Hance, K. I. Huntington, D. Jukneliene, J. Koziski, L. Mackasmiel, S. P. Mane, V. Nguyen, A. Purkayastha, J. Shallom, G. Yu, Y. Guo, J. Gabbard, D. Hix, A. F. Azad, S. C. Baker, S. M. Boyle, Y. Khudyakov, X. J. Meng, C. Rupprecht, J. Vinje, O. R. Crasta, M. J. Czar, A. Dickerman, J. D. Eckart, R. Kenyon, R. Will, J. C. Setubal, and B. W. S. Sobral
PATRIC: The VBI PathoSystems Resource Integration Center
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D401-D406; doi:10.1093/nar/gkl858 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexei E. Kazakov, Michael J. Cipriano, Pavel S. Novichkov, Simon Minovitsky, Dmitry V. Vinogradov, Adam Arkin, Andrey A. Mironov, Mikhail S. Gelfand, and Inna Dubchak
RegTransBase—a database of regulatory sequences and interactions in a wide range of prokaryotic genomes
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D407-D412; doi:10.1093/nar/gkl865 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Kim Brügger
The Sulfolobus database
Nucleic Acids Research Advance Access published on November 6, 2006
Nucl. Acids Res. 2007 35: D413-D415; doi:10.1093/nar/gkl847 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chia-Hung Chang, Yu-Chung Chang, Anthony Underwood, Chien-Shun Chiou, and Cheng-Yan Kao
VNTRDB: a bacterial variable number tandem repeat locus database
Nucleic Acids Research Advance Access published on December 14, 2006
Nucl. Acids Res. 2007 35: D416-D421; doi:10.1093/nar/gkl872 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bradley I. Arshinoff, Garret Suen, Eric M. Just, Sohel M. Merchant, Warren A. Kibbe, Rex L. Chisholm, and Roy D. Welch
Xanthusbase: adapting wikipedia principles to a model organism database
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D422-D426; doi:10.1093/nar/gkl881 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, Philippa Rhodes, John Miller, Eileen Kraemer, Christian J. Stoeckert, Jr., David S. Roos, and Jessica C. Kissinger
ApiDB: integrated resources for the apicomplexan bioinformatics resource center
Nucleic Acids Research Advance Access published on November 10, 2006
Nucl. Acids Res. 2007 35: D427-D430; doi:10.1093/nar/gkl880 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Junichi Watanabe, Hiroyuki Wakaguri, Masahide Sasaki, Yutaka Suzuki, and Sumio Sugano
Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs
Nucleic Acids Research Advance Access published on December 6, 2006
Nucl. Acids Res. 2007 35: D431-D438; doi:10.1093/nar/gkl1039 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Olivier Arnaiz, Scott Cain, Jean Cohen, and Linda Sperling
ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data
Nucleic Acids Research Advance Access published on November 16, 2006
Nucl. Acids Res. 2007 35: D439-D444; doi:10.1093/nar/gkl777 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Emmet A. O'Brien, Liisa B. Koski, Yue Zhang, LiuSong Yang, Eric Wang, Michael W. Gray, Gertraud Burger, and B. Franz Lang
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)
Nucl. Acids Res. 2007 35: D445-D451; doi:10.1093/nar/gkl770 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Prachi Shah, Gail Binkley, Christopher Lane, Stuart R. Miyasato, and Gavin Sherlock
Sequence resources at the Candida Genome Database
Nucleic Acids Research Advance Access published on November 7, 2006
Nucl. Acids Res. 2007 35: D452-D456; doi:10.1093/nar/gkl899 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]