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Front-Matter/Back-Matter Nucleic Acids Research: VOLUME 37 DATABASE ISSUE JANUARY 1, 2009 PMCID: PMC2686517 Nucleic Acids Res. 2009 January; 37(Database issue): ii. Published online 2009 January. doi: 10.1093/nar/gkn1016.PMCID: PMC2686548 Nucleic Acids Res. 2009 January; 37(Database issue): iii. Published online 2009 January. doi: 10.1093/nar/gkn1021.PMCID: PMC2686609 Articles Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009 Michael Y. Galperin and Guy R. Cochrane PMCID: PMC2686608 Database resources of the National Center for Biotechnology Information Eric W. Sayers, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, Ilene Mizrachi, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Stephen T. Sherry, Martin Shumway, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko, and Jian Ye PMCID: PMC2686545 DDBJ dealing with mass data produced by the second generation sequencer Hideaki Sugawara, Kazuho Ikeo, Satoshi Fukuchi, Takashi Gojobori, and Yoshio Tateno PMCID: PMC2686496 Petabyte-scale innovations at the European Nucleotide Archive Guy Cochrane, Ruth Akhtar, James Bonfield, Lawrence Bower, Fehmi Demiralp, Nadeem Faruque, Richard Gibson, Gemma Hoad, Tim Hubbard, Christopher Hunter, Mikyung Jang, Szilveszter Juhos, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Sheila Plaister, Rajesh Radhakrishnan, Stephen Robinson, Siamak Sobhany, Petra Ten Hoopen, Robert Vaughan, Vadim Zalunin, and Ewan Birney PMCID: PMC2686451 GenBank Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and Eric W. Sayers PMCID: PMC2686462 NCBI Reference Sequences: current status, policy and new initiatives Kim D. Pruitt, Tatiana Tatusova, William Klimke, and Donna R. Maglott PMCID: PMC2686572 DiProDB: a database for dinucleotide properties Maik Friedel, Swetlana Nikolajewa, Jürgen Sühnel, and Thomas Wilhelm PMCID: PMC2686603 UCbase & miRfunc: a database of ultraconserved sequences and microRNA function Cristian Taccioli, Enrica Fabbri, Rosa Visone, Stefano Volinia, George A. Calin, Louise Y. Fong, Roberto Gambari, Arianna Bottoni, Mario Acunzo, John Hagan, Marilena V. Iorio, Claudia Piovan, Giulia Romano, and Carlo Maria Croce PMCID: PMC2686429 MachiBase: a Drosophila melanogaster 5′-end mRNA transcription database Budrul Ahsan, Taro L. Saito, Shin-ichi Hashimoto, Keigo Muramatsu, Manabu Tsuda, Atsushi Sasaki, Kouji Matsushima, Toshiro Aigaki, and Shinichi Morishita PMCID: PMC2686457 The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences Elodie Portales-Casamar, David Arenillas, Jonathan Lim, Magdalena I. Swanson, Steven Jiang, Anthony McCallum, Stefan Kirov, and Wyeth W. Wasserman PMCID: PMC2686574 PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes Andreas Grote, Johannes Klein, Ida Retter, Isam Haddad, Susanne Behling, Boyke Bunk, Ilona Biegler, Svitlana Yarmolinetz, Dieter Jahn, and Richard Münch PMCID: PMC2686542 PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes Logan Everett, Antony Vo, and Sridhar Hannenhalli PMCID: PMC2686453 Transterm: a database to aid the analysis of regulatory sequences in mRNAs Grant H. Jacobs, Augustine Chen, Stewart G. Stevens, Peter A. Stockwell, Michael A. Black, Warren P. Tate, and Chris M. Brown PMCID: PMC2686486 UniPROBE: an online database of protein binding microarray data on protein–DNA interactions Daniel E. Newburger and Martha L. Bulyk PMCID: PMC2686578 BPS: a database of RNA base-pair structures Yurong Xin and Wilma K. Olson PMCID: PMC2686499 The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs Toutai Mituyama, Kouichirou Yamada, Emi Hattori, Hiroaki Okida, Yukiteru Ono, Goro Terai, Aya Yoshizawa, Takashi Komori, and Kiyoshi Asai PMCID: PMC2686472 GtRNAdb: a database of transfer RNA genes detected in genomic sequence Patricia P. Chan and Todd M. Lowe PMCID: PMC2686519 miR2Disease: a manually curated database for microRNA deregulation in human disease Qinghua Jiang, Yadong Wang, Yangyang Hao, Liran Juan, Mingxiang Teng, Xinjun Zhang, Meimei Li, Guohua Wang, and Yunlong Liu PMCID: PMC2686559 miRecords: an integrated resource for microRNA–target interactions Feifei Xiao, Zhixiang Zuo, Guoshuai Cai, Shuli Kang, Xiaolian Gao, and Tongbin Li PMCID: PMC2686554 miROrtho: computational survey of microRNA genes Daniel Gerlach, Evgenia V. Kriventseva, Nazim Rahman, Charles E. Vejnar, and Evgeny M. Zdobnov PMCID: PMC2686488 MODOMICS: a database of RNA modification pathways. 2008 update Anna Czerwoniec, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Katarzyna H. Kaminska, Joanna M. Kasprzak, Janusz M. Bujnicki, Henri Grosjean, and Kristian Rother PMCID: PMC2686465 NRED: a database of long noncoding RNA expression Marcel E. Dinger, Ken C. Pang, Tim R. Mercer, Mark L. Crowe, Sean M. Grimmond, and John S. Mattick PMCID: PMC2686506 PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots Michela Taufer, Abel Licon, Roberto Araiza, David Mireles, F. H. D. van Batenburg, Alexander P. Gultyaev, and Ming-Ying Leung PMCID: PMC2686561 Rfam: updates to the RNA families database Paul P. Gardner, Jennifer Daub, John G. Tate, Eric P. Nawrocki, Diana L. Kolbe, Stinus Lindgreen, Adam C. Wilkinson, Robert D. Finn, Sam Griffiths-Jones, Sean R. Eddy, and Alex Bateman PMCID: PMC2686503 The Ribosomal Database Project: improved alignments and new tools for rRNA analysis J. R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity, and J. M. Tiedje PMCID: PMC2686447 siRecords: a database of mammalian RNAi experiments and efficacies Yongliang Ren, Wuming Gong, Haiyan Zhou, Yejun Wang, Feifei Xiao, and Tongbin Li PMCID: PMC2686443 sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes Hsi-Yuan Huang, Heng-Yi Chang, Chih-Hung Chou, Ching-Ping Tseng, Shinn-Ying Ho, Chi-Dung Yang, Yih-Wei Ju, and Hsien-Da Huang PMCID: PMC2686527 The database of experimentally supported targets: a functional update of TarBase Giorgos L. Papadopoulos, Martin Reczko, Victor A. Simossis, Praveen Sethupathy, and Artemis G. Hatzigeorgiou PMCID: PMC2686456 tRNAdb 2009: compilation of tRNA sequences and tRNA genes Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, and Joern Pütz PMCID: PMC2686557 tRNADB-CE: tRNA gene database curated manually by experts Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, and Hachiro Inokuchi PMCID: PMC2686568 The Universal Protein Resource (UniProt) 2009 The UniProt Consortium PMCID: PMC2686606 CentrosomeDB: a human centrosomal proteins database Rubén Nogales-Cadenas, Federico Abascal, Javier Díez-Pérez, José María Carazo, and Alberto Pascual-Montano PMCID: PMC2686521 NOPdb: Nucleolar Proteome Database—2008 update Yasmeen Ahmad, François-Michel Boisvert, Peter Gregor, Andy Cobley, and Angus I. Lamond PMCID: PMC2686505 Minimotif miner 2nd release: a database and web system for motif search Sanguthevar Rajasekaran, Sudha Balla, Patrick Gradie, Michael R. Gryk, Krishna Kadaveru, Vamsi Kundeti, Mark W. Maciejewski, Tian Mi, Nicholas Rubino, Jay Vyas, and Martin R. Schiller PMCID: PMC2686579 SDR: a database of predicted specificity-determining residues in proteins Jason E. Donald and Eugene I. Shakhnovich PMCID: PMC2686543 SuperSite: dictionary of metabolite and drug binding sites in proteins Raphael André Bauer, Stefan Günther, Dominic Jansen, Carolin Heeger, Paul Florian Thaben, and Robert Preissner PMCID: PMC2686477 TMFunction: database for functional residues in membrane proteins M. Michael Gromiha, Yukimitsu Yabuki, M. Xavier Suresh, A. Mary Thangakani, Makiko Suwa, and Kazuhiko Fukui PMCID: PMC2686444 CDD: specific functional annotation with the Conserved Domain Database Aron Marchler-Bauer, John B. Anderson, Farideh Chitsaz, Myra K. Derbyshire, Carol DeWeese-Scott, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H. Marchler, Mikhail Mullokandov, James S. Song, Asba Tasneem, Narmada Thanki, Roxanne A. Yamashita, Dachuan Zhang, Naigong Zhang, and Stephen H. Bryant PMCID: PMC2686570 InterPro: the integrative protein signature database Sarah Hunter, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, Louise Daugherty, Lauranne Duquenne, Robert D. Finn, Julian Gough, Daniel Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Aurélie Laugraud, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Jaina Mistry, Alex Mitchell, Nicola Mulder, Darren Natale, Christine Orengo, Antony F. Quinn, Jeremy D. Selengut, Christian J. A. Sigrist, Manjula Thimma, Paul D. Thomas, Franck Valentin, Derek Wilson, Cathy H. Wu, and Corin Yeats PMCID: PMC2686546 The National Center for Biotechnology Information's Protein Clusters Database William Klimke, Richa Agarwala, Azat Badretdin, Slava Chetvernin, Stacy Ciufo, Boris Fedorov, Boris Kiryutin, Kathleen O’Neill, Wolfgang Resch, Sergei Resenchuk, Susan Schafer, Igor Tolstoy, and Tatiana Tatusova PMCID: PMC2686591 Protein segment finder: an online search engine for segment motifs in the PDB Abraham O. Samson and Michael Levitt PMCID: PMC2686524 SMART 6: recent updates and new developments Ivica Letunic, Tobias Doerks, and Peer Bork PMCID: PMC2686533 The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics Brandi L. Cantarel, Pedro M. Coutinho, Corinne Rancurel, Thomas Bernard, Vincent Lombard, and Bernard Henrissat PMCID: PMC2686590 The Degradome database: mammalian proteases and diseases of proteolysis Víctor Quesada, Gonzalo R. Ordóñez, Luis M. Sánchez, Xose S. Puente, and Carlos López-Otín PMCID: PMC2686449 Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases David M. A. Martin, Diego Miranda-Saavedra, and Geoffrey J. Barton PMCID: PMC2686601 OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules Chuan-Yun Li, Qing-Rong Liu, Ping-Wu Zhang, Xiao-Mo Li, Liping Wei, and George R. Uhl PMCID: PMC2686464 PeroxiBase: a database with new tools for peroxidase family classification Dominique Koua, Lorenzo Cerutti, Laurent Falquet, Christian J. A. Sigrist, Grégory Theiler, Nicolas Hulo, and Christophe Dunand PMCID: PMC2686439 SysZNF: the C2H2 zinc finger gene database Guohui Ding, Peter Lorenz, Michael Kreutzer, Yixue Li, and Hans-Juergen Thiesen PMCID: PMC2686507 The Transporter Classification Database: recent advances Milton H. Saier, Jr, Ming Ren Yen, Keith Noto, Dorjee G. Tamang, and Charles Elkan PMCID: PMC2686586 Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays Fengli Fu, Jeffry D. Sander, Morgan Maeder, Stacey Thibodeau-Beganny, J. Keith Joung, Drena Dobbs, Leslie Miller, and Daniel F. Voytas PMCID: PMC2686427 MMsINC: a large-scale chemoinformatics database Joel Masciocchi, Gianfranco Frau, Marco Fanton, Mattia Sturlese, Matteo Floris, Luca Pireddu, Piergiorgio Palla, Fabian Cedrati, Patricia Rodriguez-Tomé, and Stefano Moro PMCID: PMC2686567 SuperScent—a database of flavors and scents Mathias Dunkel, Ulrike Schmidt, Swantje Struck, Lena Berger, Bjoern Gruening, Julia Hossbach, Ines S. Jaeger, Uta Effmert, Birgit Piechulla, Roger Eriksson, Jette Knudsen, and Robert Preissner PMCID: PMC2686498 SuperToxic: a comprehensive database of toxic compounds Ulrike Schmidt, Swantje Struck, Bjoern Gruening, Julia Hossbach, Ines S. Jaeger, Roza Parol, Ulrike Lindequist, Eberhard Teuscher, and Robert Preissner PMCID: PMC2686515 3did Update: domain–domain and peptide-mediated interactions of known 3D structure Amelie Stein, Alejandro Panjkovich, and Patrick Aloy PMCID: PMC2686500 AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse Masafumi Shionyu, Akihiro Yamaguchi, Kazuki Shinoda, Ken-ichi Takahashi, and Mitiko Go PMCID: PMC2686549 The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies Alison L. Cuff, Ian Sillitoe, Tony Lewis, Oliver C. Redfern, Richard Garratt, Janet Thornton, and Christine A. Orengo PMCID: PMC2686597 CC+: a relational database of coiled-coil structures Oliver D. Testa, Efrosini Moutevelis, and Derek N. Woolfson PMCID: PMC2686509 The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures Ofir Goldenberg, Elana Erez, Guy Nimrod, and Nir Ben-Tal PMCID: PMC2686473 CPDB: a database of circular permutation in proteins Wei-Cheng Lo, Chi-Ching Lee, Che-Yu Lee, and Ping-Chiang Lyu PMCID: PMC2686539 The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions Satoshi Fukuchi, Keiichi Homma, Shigetaka Sakamoto, Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori, and Ken Nishikawa PMCID: PMC2686575 JAIL: a structure-based interface library for macromolecules Stefan Günther, Joachim von Eichborn, Patrick May, and Robert Preissner PMCID: PMC2686555 KineticDB: a database of protein folding kinetics Natalya S. Bogatyreva, Alexander A. Osypov, and Dmitry N. Ivankov PMCID: PMC2686587 modbase, a database of annotated comparative protein structure models and associated resources Ursula Pieper, Narayanan Eswar, Ben M. Webb, David Eramian, Libusha Kelly, David T. Barkan, Hannah Carter, Parminder Mankoo, Rachel Karchin, Marc A. Marti-Renom, Fred P. Davis, and Andrej Sali PMCID: PMC2686492 PDBsum new things Roman A. Laskowski PMCID: PMC2686501 PiSite: a database of protein interaction sites using multiple binding states in the PDB Miho Higurashi, Takashi Ishida, and Kengo Kinoshita PMCID: PMC2686547 The protein structure initiative structural genomics knowledgebase Helen M. Berman, John D. Westbrook, Margaret J. Gabanyi, Wendy Tao, Raship Shah, Andrei Kouranov, Torsten Schwede, Konstantin Arnold, Florian Kiefer, Lorenza Bordoli, Jürgen Kopp, Michael Podvinec, Paul D. Adams, Lester G. Carter, Wladek Minor, Rajesh Nair, and Joshua La Baer PMCID: PMC2686438 RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases Alexandra Shulman-Peleg, Ruth Nussinov, and Haim J. Wolfson PMCID: PMC2686467 SPROUTS: a database for the evaluation of protein stability upon point mutation Mathieu Lonquety, Zoé Lacroix, Nikolaos Papandreou, and Jacques Chomilier PMCID: PMC2686433 SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny Derek Wilson, Ralph Pethica, Yiduo Zhou, Charles Talbot, Christine Vogel, Martin Madera, Cyrus Chothia, and Julian Gough PMCID: PMC2686452 The SWISS-MODEL Repository and associated resources Florian Kiefer, Konstantin Arnold, Michael Künzli, Lorenza Bordoli, and Torsten Schwede PMCID: PMC2686475 Voronoia: analyzing packing in protein structures Kristian Rother, Peter Werner Hildebrand, Andrean Goede, Bjoern Gruening, and Robert Preissner PMCID: PMC2686436 The GOA database in 2009—an integrated Gene Ontology Annotation resource Daniel Barrell, Emily Dimmer, Rachael P. Huntley, David Binns, Claire O’Donovan, and Rolf Apweiler PMCID: PMC2686469 Selectome: a database of positive selection Estelle Proux, Romain A. Studer, Sébastien Moretti, and Marc Robinson-Rechavi PMCID: PMC2686563 PEDANT covers all complete RefSeq genomes Mathias C. Walter, Thomas Rattei, Roland Arnold, Ulrich Güldener, Martin Münsterkötter, Karamfilka Nenova, Gabi Kastenmüller, Patrick Tischler, Andreas Wölling, Andreas Volz, Norbert Pongratz, Ralf Jost, Hans-Werner Mewes, and Dmitrij Frishman PMCID: PMC2686588 STRING 8—a global view on proteins and their functional interactions in 630 organisms Lars J. Jensen, Michael Kuhn, Manuel Stark, Samuel Chaffron, Chris Creevey, Jean Muller, Tobias Doerks, Philippe Julien, Alexander Roth, Milan Simonovic, Peer Bork, and Christian von Mering PMCID: PMC2686466 Human immunodeficiency virus type 1, human protein interaction database at NCBI William Fu, Brigitte E. Sanders-Beer, Kenneth S. Katz, Donna R. Maglott, Kim D. Pruitt, and Roger G. Ptak PMCID: PMC2686594 Influenza sequence and epitope database Seok Yang, Joo-Yeon Lee, Joon Seung Lee, Wayne P. Mitchell, Hee-Bok Oh, Chun Kang, and Kyung Hyun Kim PMCID: PMC2686482 The RNA Virus Database Robert Belshaw, Tulio de Oliveira, Sidney Markowitz, and Andrew Rambaut PMCID: PMC2686580 VIPERdb2: an enhanced and web API enabled relational database for structural virology Mauricio Carrillo-Tripp, Craig M. Shepherd, Ian A. Borelli, Sangita Venkataraman, Gabriel Lander, Padmaja Natarajan, John E. Johnson, Charles L. Brooks, III, and Vijay S. Reddy PMCID: PMC2686430 ARDB—Antibiotic Resistance Genes Database Bo Liu and Mihai Pop PMCID: PMC2686595 ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes Pavel S. Novichkov, Igor Ratnere, Yuri I. Wolf, Eugene V. Koonin, and Inna Dubchak PMCID: PMC2686458 DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes Ren Zhang and Yan Lin PMCID: PMC2686491 DOOR: a database for prokaryotic operons Fenglou Mao, Phuongan Dam, Jacky Chou, Victor Olman, and Ying Xu PMCID: PMC2686520 EcoCyc: A comprehensive view of Escherichia coli biology Ingrid M. Keseler, César Bonavides-Martínez, Julio Collado-Vides, Socorro Gama-Castro, Robert P. Gunsalus, D. Aaron Johnson, Markus Krummenacker, Laura M. Nolan, Suzanne Paley, Ian T. Paulsen, Martin Peralta-Gil, Alberto Santos-Zavaleta, Alexander Glennon Shearer, and Peter D. Karp PMCID: PMC2686493 HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot Tania Lima, Andrea H. Auchincloss, Elisabeth Coudert, Guillaume Keller, Karine Michoud, Catherine Rivoire, Virginie Bulliard, Edouard de Castro, Corinne Lachaize, Delphine Baratin, Isabelle Phan, Lydie Bougueleret, and Amos Bairoch PMCID: PMC2686602 OperonDB: a comprehensive database of predicted operons in microbial genomes Mihaela Pertea, Kunmi Ayanbule, Megan Smedinghoff, and Steven L. Salzberg PMCID: PMC2686487 Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes Geoffrey L. Winsor, Thea Van Rossum, Raymond Lo, Bhavjinder Khaira, Matthew D. Whiteside, Robert E. W. Hancock, and Fiona S. L. Brinkman PMCID: PMC2686508 rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea Zarraz May-Ping Lee, Carl Bussema, III, and Thomas M. Schmidt PMCID: PMC2686494 Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform ‘Open Genome Resource’ (OGeR) Johannes Klein, Richard Münch, Ilona Biegler, Isam Haddad, Ida Retter, and Dieter Jahn PMCID: PMC2686516 TB database: an integrated platform for tuberculosis research T. B. K. Reddy, Robert Riley, Farrell Wymore, Phillip Montgomery, Dave DeCaprio, Reinhard Engels, Marcel Gellesch, Jeremy Hubble, Dennis Jen, Heng Jin, Michael Koehrsen, Lisa Larson, Maria Mao, Michael Nitzberg, Peter Sisk, Christian Stolte, Brian Weiner, Jared White, Zachariah K. Zachariah, Gavin Sherlock, James E. Galagan, Catherine A. Ball, and Gary K. Schoolnik PMCID: PMC2686437 Aspergillus Genomes and the Aspergillus Cloud Jane E. Mabey Gilsenan, Graham Atherton, Jennifer Bartholomew, Peter F. Giles, Teresa K. Attwood, David W. Denning, and Paul Bowyer PMCID: PMC2686514 dictyBase—a Dictyostelium bioinformatics resource update Petra Fey, Pascale Gaudet, Tomaz Curk, Blaz Zupan, Eric M. Just, Siddhartha Basu, Sohel N. Merchant, Yulia A. Bushmanova, Gad Shaulsky, Warren A. Kibbe, and Rex L. Chisholm PMCID: PMC2686522 Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009 Hiroyuki Wakaguri, Yutaka Suzuki, Toshiaki Katayama, Shuichi Kawashima, Eri Kibukawa, Kazushi Hiranuka, Masahide Sasaki, Sumio Sugano, and Junichi Watanabe PMCID: PMC2686583 GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jane M. Carlton, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, John A. Miller, Hilary G. Morrison, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Christian J. Stoeckert, Jr, Steven Sullivan, Charles Treatman, and Haiming Wang PMCID: PMC2686445 metaTIGER: a metabolic evolution resource John W. Whitaker, Ivica Letunic, Glenn A. McConkey, and David R. Westhead PMCID: PMC2686446 PlasmoDB: a functional genomic database for malaria parasites Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao, Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei Li, John A. Miller, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Christian J. Stoeckert, Jr., Charles Treatman, and Haiming Wang PMCID: PMC2686598 TcSNP: a database of genetic variation in Trypanosoma cruzi Alejandro A. Ackermann, Santiago J. Carmona, and Fernán Agüero PMCID: PMC2686512 Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes David J. Sherman, Tiphaine Martin, Macha Nikolski, Cyril Cayla, Jean-Luc Souciet, and Pascal Durrens PMCID: PMC2686504 FlyBase: enhancing Drosophila Gene Ontology annotations Susan Tweedie, Michael Ashburner, Kathleen Falls, Paul Leyland, Peter McQuilton, Steven Marygold, Gillian Millburn, David Osumi-Sutherland, Andrew Schroeder, Ruth Seal, Haiyan Zhang, and The FlyBase Consortium PMCID: PMC2686450 FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution Andrei Pisarev, Ekaterina Poustelnikova, Maria Samsonova, and John Reinitz PMCID: PMC2686593 FLYSNPdb: a high-density SNP database of Drosophila melanogaster Doris Chen, Jürg Berger, Michaela Fellner, and Takashi Suzuki PMCID: PMC2686552 Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics John Martin, Sahar Abubucker, Todd Wylie, Yong Yin, Zhengyuan Wang, and Makedonka Mitreva PMCID: PMC2686480 SchistoDB: a Schistosoma mansoni genome resource Adhemar Zerlotini, Mark Heiges, Haiming Wang, Romulo L. V. Moraes, Anderson J. Dominitini, Jerônimo C. Ruiz, Jessica C. Kissinger, and Guilherme Oliveira PMCID: PMC2686589 VectorBase: a data resource for invertebrate vector genomics Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, Martin Hammond, Catherine A. Hill, Nathan Konopinski, Neil F. Lobo, Robert M. MacCallum, Greg Madey, Karine Megy, Jason Meyer, Seth Redmond, David W. Severson, Eric O. Stinson, Pantelis Topalis, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, and Frank H. Collins PMCID: PMC2686483 BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 Antje Chang, Maurice Scheer, Andreas Grote, Ida Schomburg, and Dietmar Schomburg PMCID: PMC2686525 ExplorEnz: the primary source of the IUBMB enzyme list Andrew G. McDonald, Sinéad Boyce, and Keith F. Tipton PMCID: PMC2686581 Bionemo: molecular information on biodegradation metabolism Guillermo Carbajosa, Almudena Trigo, Alfonso Valencia, and Ildefonso Cases PMCID: PMC2686592 HMDB: a knowledgebase for the human metabolome David S. Wishart, Craig Knox, An Chi Guo, Roman Eisner, Nelson Young, Bijaya Gautam, David D. Hau, Nick Psychogios, Edison Dong, Souhaila Bouatra, Rupasri Mandal, Igor Sinelnikov, Jianguo Xia, Leslie Jia, Joseph A. Cruz, Emilia Lim, Constance A. Sobsey, Savita Shrivastava, Paul Huang, Philip Liu, Lydia Fang, Jun Peng, Ryan Fradette, Dean Cheng, Dan Tzur, Melisa Clements, Avalyn Lewis, Andrea De Souza, Azaret Zuniga, Margot Dawe, Yeping Xiong, Derrick Clive, Russ Greiner, Alsu Nazyrova, Rustem Shaykhutdinov, Liang Li, Hans J. Vogel, and Ian Forsythe PMCID: PMC2686599 PMAP: databases for analyzing proteolytic events and pathways Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael Blinov, Salmaz S. Ibragimova, Sarah Boyd, Boris Ratnikov, Piotr Cieplak, Adam Godzik, Jeffrey W. Smith, Andrei L. Osterman, and Alexey M. Eroshkin PMCID: PMC2686432 Reactome knowledgebase of human biological pathways and processes Lisa Matthews, Gopal Gopinath, Marc Gillespie, Michael Caudy, David Croft, Bernard de Bono, Phani Garapati, Jill Hemish, Henning Hermjakob, Bijay Jassal, Alex Kanapin, Suzanna Lewis, Shahana Mahajan, Bruce May, Esther Schmidt, Imre Vastrik, Guanming Wu, Ewan Birney, Lincoln Stein, and Peter D’Eustachio PMCID: PMC2686536 ConsensusPathDB—a database for integrating human functional interaction networks Atanas Kamburov, Christoph Wierling, Hans Lehrach, and Ralf Herwig PMCID: PMC2686562 EcID. A database for the inference of functional interactions in E. coli Eduardo Andres Leon, Iakes Ezkurdia, Beatriz García, Alfonso Valencia, and David Juan PMCID: PMC2686479 Update of KDBI: Kinetic Data of Bio-molecular Interaction database Pankaj Kumar, B. C. Han, Z. Shi, J. Jia, Y. P. Wang, Y. T. Zhang, L. Liang, Q. F. Liu, Z. L. Ji, and Y. Z. Chen PMCID: PMC2686478 Michigan molecular interactions r2: from interacting proteins to pathways V. Glenn Tarcea, Terry Weymouth, Alex Ade, Aaron Bookvich, Jing Gao, Vasudeva Mahavisno, Zach Wright, Adriane Chapman, Magesh Jayapandian, Arzucan Özgür, Yuanyuan Tian, Jim Cavalcoli, Barbara Mirel, Jignesh Patel, Dragomir Radev, Brian Athey, David States, and H. V. Jagadish PMCID: PMC2686565 PIG—the pathogen interaction gateway Tim Driscoll, Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral PMCID: PMC2686532 PIPs: human protein–protein interaction prediction database Mark D. McDowall, Michelle S. Scott, and Geoffrey J. Barton PMCID: PMC2686497 UniHI 4: new tools for query, analysis and visualization of the human protein–protein interactome Gautam Chaurasia, Soniya Malhotra, Jenny Russ, Sigrid Schnoegl, Christian Hänig, Erich E. Wanker, and Matthias E. Futschik PMCID: PMC2686569 VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus–host interaction networks Vincent Navratil, Benoît de Chassey, Laurène Meyniel, Stéphane Delmotte, Christian Gautier, Patrice André, Vincent Lotteau, and Chantal Rabourdin-Combe PMCID: PMC2686459 VirusMINT: a viral protein interaction database Andrew Chatr-aryamontri, Arnaud Ceol, Daniele Peluso, Aurelio Nardozza, Simona Panni, Francesca Sacco, Michele Tinti, Alex Smolyar, Luisa Castagnoli, Marc Vidal, Michael E. Cusick, and Gianni Cesareni PMCID: PMC2686573 PID: the Pathway Interaction Database Carl F. Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay, and Kenneth H. Buetow PMCID: PMC2686461 IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels Anthony J. Harmar, Rebecca A. Hills, Edward M. Rosser, Martin Jones, O. Peter Buneman, Donald R. Dunbar, Stuart D. Greenhill, Valerie A. Hale, Joanna L. Sharman, Tom I. Bonner, William A. Catterall, Anthony P. Davenport, Philippe Delagrange, Colin T. Dollery, Steven M. Foord, George A. Gutman, Vincent Laudet, Richard R. Neubig, Eliot H. Ohlstein, Richard W. Olsen, John Peters, Jean-Philippe Pin, Robert R. Ruffolo, David B. Searls, Mathew W. Wright, and Michael Spedding PMCID: PMC2686540 CleanEST: a database of cleansed EST libraries Byungwook Lee and Gwangsik Shin PMCID: PMC2686460 Ensembl 2009 T. J. P. Hubbard, B. L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, G. Coates, S. Fairley, S. Fitzgerald, J. Fernandez-Banet, L. Gordon, S. Graf, S. Haider, M. Hammond, R. Holland, K. Howe, A. Jenkinson, N. Johnson, A. Kahari, D. Keefe, S. Keenan, R. Kinsella, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, D. Rios, M. Schuster, G. Slater, D. Smedley, W. Spooner, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, S. Wilder, A. Zadissa, E. Birney, F. Cunningham, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, A. Kasprzyk, G. Proctor, J. Smith, S. Searle, and P. Flicek PMCID: PMC2686571 EVOG: a database for evolutionary analysis of overlapping genes Dae-Soo Kim, Chi-Young Cho, Jae-Won Huh, Heui-Soo Kim, and Hwan-Gue Cho PMCID: PMC2686455 ExDom: an integrated database for comparative analysis of the exon–intron structures of protein domains in eukaryotes Ashwini Bhasi, Philge Philip, Vinu Manikandan, and Periannan Senapathy PMCID: PMC2686582 The Mouse Genome Database genotypes::phenotypes Judith A. Blake, Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, and the Mouse Genome Database Group PMCID: PMC2686566 Mouse Phenome Database Stephen C. Grubb, Terry P. Maddatu, Carol J. Bult, and Molly A. Bogue PMCID: PMC2686531 PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood Tim Hulsen, Peter M. A. Groenen, Jacob de Vlieg, and Wynand Alkema PMCID: PMC2686476 Pseudofam: the pseudogene families database Hugo Y. K. Lam, Ekta Khurana, Gang Fang, Philip Cayting, Nicholas Carriero, Kei-Hoi Cheung, and Mark B. Gerstein PMCID: PMC2686518 The Rat Genome Database 2009: variation, ontologies and pathways Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu Bakir-Gungor, Jeffrey DePons, Stanley Laulederkind, Timothy Lowry, Rajni Nigram, Victoria Petri, Jennifer Smith, Alexander Stoddard, Simon N. Twigger, and Howard J. Jacob PMCID: PMC2686558 SpBase: the sea urchin genome database and web site R. Andrew Cameron, Manoj Samanta, Autumn Yuan, Dong He, and Eric Davidson PMCID: PMC2686435 The UCSC Genome Browser Database: update 2009 R. M. Kuhn, D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, M. Pheasant, L. Meyer, F. Hsu, A. S. Hinrichs, R. A. Harte, B. Giardine, P. Fujita, M. Diekhans, T. Dreszer, H. Clawson, G. P. Barber, D. Haussler, and W. J. Kent PMCID: PMC2686463 Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics Yukio Maruyama, Ai Wakamatsu, Yoshifumi Kawamura, Kouichi Kimura, Jun-ichi Yamamoto, Tetsuo Nishikawa, Yasutomo Kisu, Sumio Sugano, Naoki Goshima, Takao Isogai, and Nobuo Nomura PMCID: PMC2686585 Human Protein Reference Database—2009 update T. S. Keshava Prasad, Renu Goel, Kumaran Kandasamy, Shivakumar Keerthikumar, Sameer Kumar, Suresh Mathivanan, Deepthi Telikicherla, Rajesh Raju, Beema Shafreen, Abhilash Venugopal, Lavanya Balakrishnan, Arivusudar Marimuthu, Sutopa Banerjee, Devi S. Somanathan, Aimy Sebastian, Sandhya Rani, Somak Ray, C. J. Harrys Kishore, Sashi Kanth, Mukhtar Ahmed, Manoj K. Kashyap, Riaz Mohmood, Y. L. Ramachandra, V. Krishna, B. Abdul Rahiman, Sujatha Mohan, Prathibha Ranganathan, Subhashri Ramabadran, Raghothama Chaerkady, and Akhilesh Pandey PMCID: PMC2686490 Human Proteinpedia: a unified discovery resource for proteomics research Kumaran Kandasamy, Shivakumar Keerthikumar, Renu Goel, Suresh Mathivanan, Nandini Patankar, Beema Shafreen, Santosh Renuse, Harsh Pawar, Y. L. Ramachandra, Pradip Kumar Acharya, Prathibha Ranganathan, Raghothama Chaerkady, T. S. Keshava Prasad, and Akhilesh Pandey PMCID: PMC2686511 BodyParts3D: 3D structure database for anatomical concepts Nobutaka Mitsuhashi, Kaori Fujieda, Takuro Tamura, Shoko Kawamoto, Toshihisa Takagi, and Kousaku Okubo PMCID: PMC2686534 Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks Allan Peter Davis, Cynthia G. Murphy, Cynthia A. Saraceni-Richards, Michael C. Rosenstein, Thomas C. Wiegers, and Carolyn J. Mattingly PMCID: PMC2686584 McKusick's Online Mendelian Inheritance in Man (OMIM®) Joanna Amberger, Carol A. Bocchini, Alan F. Scott, and Ada Hamosh PMCID: PMC2686440 HGVbaseG2P: a central genetic association database Gudmundur A. Thorisson, Owen Lancaster, Robert C. Free, Robert K. Hastings, Pallavi Sarmah, Debasis Dash, Samir K. Brahmachari, and Anthony J. Brookes PMCID: PMC2686551 SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system Alexander R. Pico, Ivan V. Smirnov, Jeffrey S. Chang, Ru-Fang Yeh, Joseph L. Wiemels, John K. Wiencke, Tarik Tihan, Bruce R. Conklin, and Margaret Wrensch PMCID: PMC2686434 VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts Makoto K. Shimada, Ryuzou Matsumoto, Yosuke Hayakawa, Ryoko Sanbonmatsu, Craig Gough, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Tadashi Imanishi, and Takashi Gojobori PMCID: PMC2686441 CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens Luiz Gonzaga Almeida, Noboru J. Sakabe, Alice R. deOliveira, Maria Cristina C. Silva, Alex S. Mundstein, Tzeela Cohen, Yao-Tseng Chen, Ramon Chua, Sita Gurung, Sacha Gnjatic, Achim A. Jungbluth, Otávia L. Caballero, Amos Bairoch, Eva Kiesler, Sarah L. White, Andrew J. G. Simpson, Lloyd J. Old, Anamaria A. Camargo, and Ana Tereza R. Vasconcelos PMCID: PMC2686577 Database for exploration of functional context of genes implicated in ovarian cancer Mandeep Kaur, Aleksandar Radovanovic, Magbubah Essack, Ulf Schaefer, Monique Maqungo, Tracey Kibler, Sebastian Schmeier, Alan Christoffels, Kothandaraman Narasimhan, Mahesh Choolani, and Vladimir B. Bajic PMCID: PMC2686485 MoKCa database—mutations of kinases in cancer Christopher J. Richardson, Qiong Gao, Costas Mitsopoulous, Marketa Zvelebil, Laurence H. Pearl, and Frances M. G. Pearl PMCID: PMC2686448 AutDB: a gene reference resource for autism research Saumyendra N. Basu, Ravi Kollu, and Sharmila Banerjee-Basu PMCID: PMC2686502 DNAReplication: a database of information and resources for the eukaryotic DNA replication community Sue Cotterill and Stephen E. Kearsey PMCID: PMC2686454 ERGR: An ethanol-related gene resource An-Yuan Guo, Bradley T. Webb, Michael F. Miles, Mark P. Zimmerman, Kenneth S. Kendler, and Zhongming Zhao PMCID: PMC2686553 G2Cdb: the Genes to Cognition database Mike D. R. Croning, Michael C. Marshall, Peter McLaren, J. Douglas Armstrong, and Seth G. N. Grant PMCID: PMC2686544 INTERFEROME: the database of interferon regulated genes Shamith A. Samarajiwa, Sam Forster, Katie Auchettl, and Paul J. Hertzog PMCID: PMC2686605 MDPD: an integrated genetic information resource for Parkinson's disease Suisheng Tang, Zhuo Zhang, Gopalakrishnan Kavitha, Eng-King Tan, and See Kiong Ng PMCID: PMC2686576 RAPID: Resource of Asian Primary Immunodeficiency Diseases Shivakumar Keerthikumar, Rajesh Raju, Kumaran Kandasamy, Atsushi Hijikata, Subhashri Ramabadran, Lavanya Balakrishnan, Mukhtar Ahmed, Sandhya Rani, Lakshmi Dhevi N. Selvan, Devi S. Somanathan, Somak Ray, Mitali Bhattacharjee, Sashikanth Gollapudi, Y. L. Ramachandra, Sahely Bhadra, Chiranjib Bhattacharyya, Kohsuke Imai, Shigeaki Nonoyama, Hirokazu Kanegane, Toshio Miyawaki, Akhilesh Pandey, Osamu Ohara, and Sujatha Mohan PMCID: PMC2686530 ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression Helen Parkinson, Misha Kapushesky, Nikolay Kolesnikov, Gabriella Rustici, Mohammad Shojatalab, Niran Abeygunawardena, Hugo Berube, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Ele Holloway, Margus Lukk, James Malone, Roby Mani, Ekaterina Pilicheva, Tim F. Rayner, Faisal Rezwan, Anjan Sharma, Eleanor Williams, Xiangqun Zheng Bradley, Tomasz Adamusiak, Marco Brandizi, Tony Burdett, Richard Coulson, Maria Krestyaninova, Pavel Kurnosov, Eamonn Maguire, Sudeshna Guha Neogi, Philippe Rocca-Serra, Susanna-Assunta Sansone, Nataliya Sklyar, Mengyao Zhao, Ugis Sarkans, and Alvis Brazma PMCID: PMC2686529 BloodExpress: a database of gene expression in mouse haematopoiesis Diego Miranda-Saavedra, Subhajyoti De, Matthew W. Trotter, Sarah A. Teichmann, and Berthold Göttgens PMCID: PMC2686428 CleanEx: new data extraction and merging tools based on MeSH term annotation Viviane Praz and Philipp Bucher PMCID: PMC2686468 NCBI GEO: archive for high-throughput functional genomic data Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Rolf N. Muertter, and Ron Edgar PMCID: PMC2686538 GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development Tin-Lap Lee, Hoi-Hung Cheung, Janek Claus, Chandan Sastry, Sumeeta Singh, Loc Vu, Owen Rennert, and Wai-Yee Chan PMCID: PMC2686471 Implementation of GenePattern within the Stanford Microarray Database Jeremy Hubble, Janos Demeter, Heng Jin, Maria Mao, Michael Nitzberg, T. B. K. Reddy, Farrell Wymore, Zachariah K. Zachariah, Gavin Sherlock, and Catherine A. Ball PMCID: PMC2686537 MAPU 2.0: high-accuracy proteomes mapped to genomes Florian Gnad, Mario Oroshi, Ewan Birney, and Matthias Mann PMCID: PMC2686489 Sys-BodyFluid: a systematical database for human body fluid proteome research Su-Jun Li, Mao Peng, Hong Li, Bo-Shu Liu, Chuan Wang, Jia-Rui Wu, Yi-Xue Li, and Rong Zeng PMCID: PMC2686600 SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry Hong Xi, Jongsun Park, Guohui Ding, Yong-Hwan Lee, and Yixue Li PMCID: PMC2686442 Déjà vu: a database of highly similar citations in the scientific literature Mounir Errami, Zhaohui Sun, Tara C. Long, Angela C. George, and Harold R. Garner PMCID: PMC2686470 Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines Paolo Romano, Assunta Manniello, Ottavia Aresu, Massimiliano Armento, Michela Cesaro, and Barbara Parodi PMCID: PMC2686526 APD2: the updated antimicrobial peptide database and its application in peptide design Guangshun Wang, Xia Li, and Zhe Wang PMCID: PMC2686604 OligoArrayDb: pangenomic oligonucleotide microarray probe sets database Jean-Marie Rouillard and Erdogan Gulari PMCID: PMC2686523 RTPrimerDB: the portal for real-time PCR primers and probes Steve Lefever, Jo Vandesompele, Frank Speleman, and Filip Pattyn PMCID: PMC2686610 GOBASE: an organelle genome database Emmet A. O’Brien, Yue Zhang, Eric Wang, Veronique Marie, Wole Badejoko, B. Franz Lang, and Gertraud Burger PMCID: PMC2686550 AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants Chris Duran, Nikki Appleby, Terry Clark, David Wood, Michael Imelfort, Jacqueline Batley, and David Edwards PMCID: PMC2686484 GabiPD: the GABI primary database—a plant integrative ‘omics’ database Diego Mauricio Riaño-Pachón, Axel Nagel, Jost Neigenfind, Robert Wagner, Rico Basekow, Elke Weber, Bernd Mueller-Roeber, Svenja Diehl, and Birgit Kersten PMCID: PMC2686513 P3DB: a plant protein phosphorylation database Jianjiong Gao, Ganesh Kumar Agrawal, Jay J. Thelen, and Dong Xu PMCID: PMC2686431 PhytAMP: a database dedicated to antimicrobial plant peptides Riadh Hammami, Jeannette Ben Hamida, Gérard Vergoten, and Ismail Fliss PMCID: PMC2686510 PPDB, the Plant Proteomics Database at Cornell Qi Sun, Boris Zybailov, Wojciech Majeran, Giulia Friso, Paul Dominic B. Olinares, and Klaas J. van Wijk PMCID: PMC2686560 Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis Zhi-yu Peng, Xin Zhou, Linchuan Li, Xiangchun Yu, Hongjiang Li, Zhiqiang Jiang, Guangyu Cao, Mingyi Bai, Xingchun Wang, Caifu Jiang, Haibin Lu, Xianhui Hou, Lijia Qu, Zhiyong Wang, Jianru Zuo, Xiangdong Fu, Zhen Su, Songgang Li, and Hongwei Guo PMCID: PMC2686556 AthaMap, integrating transcriptional and post-transcriptional data Lorenz Bülow, Stefan Engelmann, Martin Schindler, and Reinhard Hehl PMCID: PMC2686474 ATTED-II provides coexpressed gene networks for Arabidopsis Takeshi Obayashi, Shinpei Hayashi, Motoshi Saeki, Hiroyuki Ohta, and Kengo Kinoshita PMCID: PMC2686564 OryGenesDB 2008 update: database interoperability for functional genomics of rice Gaëtan Droc, Christophe Périn, Sébastien Fromentin, and Pierre Larmande PMCID: PMC2686528 RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome Supat Thongjuea, Vinitchan Ruanjaichon, Richard Bruskiewich, and Apichart Vanavichit PMCID: PMC2686607 Update of the Diatom EST Database: a new tool for digital transcriptomics Uma Maheswari, Thomas Mock, E. Virginia Armbrust, and Chris Bowler PMCID: PMC2686495 IMGT®, the international ImMunoGeneTics information system® Marie-Paule Lefranc, Véronique Giudicelli, Chantal Ginestoux, Joumana Jabado-Michaloud, Géraldine Folch, Fatena Bellahcene, Yan Wu, Elodie Gemrot, Xavier Brochet, Jérôme Lane, Laetitia Regnier, François Ehrenmann, Gérard Lefranc, and Patrice Duroux PMCID: PMC2686541 The IMGT/HLA database James Robinson, Matthew J. Waller, Sylvie C. Fail, Hamish McWilliam, Rodrigo Lopez, Peter Parham, and Steven G. E. Marsh PMCID: PMC2686596 The HuRef Browser: a web resource for individual human genomics Nelson Axelrod, Yuan Lin, Pauline C. Ng, Timothy B. Stockwell, Jonathan Crabtree, Jiaqi Huang, Ewen Kirkness, Robert L. Strausberg, Marvin E. Frazier, J. Craig Venter, Saul Kravitz, and Samuel Levy PMCID: PMC2686481 The YH database: the first Asian diploid genome database Guoqing Li, Lijia Ma, Chao Song, Zhentao Yang, Xiulan Wang, Hui Huang, Yingrui Li, Ruiqiang Li, Xiuqing Zhang, Huanming Yang, Jian Wang, and Jun Wang PMCID: PMC2686535
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