Nucleic Acids Research, Volume 34

Volume 34, Database-Issue, January 1 2006

• Alex Bateman:
  EDITORIAL. 1
  Electronic Edition (link) BibTeX

• Michael Y. Galperin:
  The Molecular Biology Database Collection: 2006 update. 3-5
  Electronic Edition (link) BibTeX
• Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori, Yoshio Tateno:
  DDBJ in preparation for overview of research activities behind data submissions. 6-9
  Electronic Edition (link) BibTeX
• Guy Cochrane, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Wendy Baker, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Paul Browne, Alexandra van den Broek, Matias Castro, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Carola Kanz, Tamara Kulikova, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Michelle McHale, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Siamak Sobhany, Peter Stoehr, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler:
  EMBL Nucleotide Sequence Database: developments in 2005. 10-15
  Electronic Edition (link) BibTeX
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
  GenBank. 16-20
  Electronic Edition (link) BibTeX
• Namshin Kim, Pora Kim, Seungyoon Nam, Seokmin Shin, Sanghyuk Lee:
  ChimerDB - a knowledgebase for fusion sequences. 21-24
  Electronic Edition (link) BibTeX
• K. T. Nishant, Kumar Chetan, M. R. S. Rao:
  HUMHOT: a database of human meiotic recombination hot spots. 25-28
  Electronic Edition (link) BibTeX
• Rivka L. Glaser, Joshua P. Ramsay, Ian M. Morison:
  The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations. 29-31
  Electronic Edition (link) BibTeX
• P. Siguier, J. Perochon, L. Lestrade, J. Mahillon, M. Chandler:
  ISfinder: the reference centre for bacterial insertion sequences. 32-36
  Electronic Edition (link) BibTeX
• Grant H. Jacobs, Peter A. Stockwell, Warren Tate, Chris M. Brown:
  Transterm - extended search facilities and improved integration with other databases. 37-40
  Electronic Edition (link) BibTeX
• Jeremy D. Glasner, Michael Rusch, Paul Liss, Guy Plunkett III, Eric L. Cabot, Aaron E. Darling, Bradley D. Anderson, Paul Infield-Harm, Michael C. Gilson, Nicole T. Perna:
  ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. 41-45
  Electronic Edition (link) BibTeX
• Stefan Stamm, Jean-Jack M. Riethoven, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Yesheng Tang, Nuno L. Barbosa-Morais, Thangavel Alphonse Thanaraj:
  ASD: a bioinformatics resource on alternative splicing. 46-55
  Electronic Edition (link) BibTeX
• Dirk Holste, George Huo, Vivian Tung, Christopher B. Burge:
  HOLLYWOOD: a comparative relational database of alternative splicing. 56-62
  Electronic Edition (link) BibTeX
• Enrique Blanco, Domènec Farré, M. Mar Albà, Xavier Messeguer, Roderic Guigó:
  ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. 63-67
  Electronic Edition (link) BibTeX
• Gordon Robertson, Misha Bilenky, K. Lin, An He, W. Yuen, M. Dagpinar, Richard Varhol, Kevin Teague, Obi L. Griffith, X. Zhang, Y. Pan, Maik Hassel, Monica C. Sleumer, W. Pan, Erin Pleasance, M. Chuang, H. Hao, Yvonne Y. Li, Neil Robertson, C. Fjell, B. Li, Stephen Montgomery, Tamara Astakhova, Jianjun Zhou, Jörg Sander, Asim S. Siddiqui, Steven J. M. Jones:
  cisRED: a database system for genome-scale computational discovery of regulatory elements. 68-73
  Electronic Edition (link) BibTeX
• Sarah K. Kummerfeld, Sarah A. Teichmann:
  DBD: a transcription factor prediction database. 74-81
  Electronic Edition (link) BibTeX
• Christoph D. Schmid, Rouaïda Périer, Viviane Praz, Philipp Bucher:
  EPD in its twentieth year: towards complete promoter coverage of selected model organisms. 82-85
  Electronic Edition (link) BibTeX
• Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano:
  DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. 86-89
  Electronic Edition (link) BibTeX
• Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi, Philipp Bucher:
  HTPSELEX - a database of high-throughput SELEX libraries for transcription factor binding sites. 90-94
  Electronic Edition (link) BibTeX
• Dominique Vlieghe, Albin Sandelin, Pieter J. De Bleser, Kris Vleminckx, Wyeth W. Wasserman, Frans van Roy, Boris Lenhard:
  A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. 95-97
  Electronic Edition (link) BibTeX
• Hao Sun, Saranyan K. Palaniswamy, Twyla T. Pohar, Victor X. Jin, Tim Hui-Ming Huang, Ramana V. Davuluri:
  MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. 98-103
  Electronic Edition (link) BibTeX
• Xin Chen, Jian-min Wu, Klaus Hornischer, Alexander E. Kel, Edgar Wingender:
  TiProD: the Tissue-specific Promoter Database. 104-107
  Electronic Edition (link) BibTeX
• V. Matys, Olga V. Kel-Margoulis, Ellen Fricke, Ines Liebich, Sigrid Land, A. Barre-Dirrie, Ingmar Reuter, D. Chekmenev, Mathias Krull, Klaus Hornischer, Nico Voss, P. Stegmaier, Birgit Lewicki-Potapov, H. Saxel, Alexander E. Kel, Edgar Wingender:
  TRANSFAC^® and its module TRANSCompel^®: transcriptional gene regulation in eukaryotes. 108-110
  Electronic Edition (link) BibTeX
• Tala Bakheet, Bryan R. G. Williams, Khalid S. A. Khabar:
  ARED 3.0: the large and diverse AU-rich transcriptome. 111-114
  Electronic Edition (link) BibTeX
• Priyanka Shahi, Serguei Loukianiouk, Andreas Bohne-Lang, Marc Kenzelmann, Stefan Küffer, Sabine Maertens, Roland Eils, Hermann-Josef Gröne, Norbert Gretz, Benedikt Brors:
  Argonaute - a database for gene regulation by mammalian microRNAs. 115-118
  Electronic Edition (link) BibTeX
• Rumen Kostadinov, Nishtha Malhotra, Manuel Viotti, Robert Shine, Lawrence D'Antonio, Paramjeet Bagga:
  GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. 119-124
  Electronic Edition (link) BibTeX
• Martin Mokrejs, Václav Vopálensky, Ondrej Kolenaty, Tomás Masek, Zuzana Feketová, Petra Sekyrová, Barbora Skaloudová, Vítezslav Kríz, Martin Pospísek:
  IRESite: the database of experimentally verified IRES structures (www.iresite.org). 125-130
  Electronic Edition (link) BibTeX
• Liliana R. Stefan, Rui Zhang, Aaron G. Levitan, Donna K. Hendrix, Steven E. Brenner, Stephen R. Holbrook:
  MeRNA: a database of metal ion binding sites in RNA structures. 131-134
  Electronic Edition (link) BibTeX
• Paul Wei-Che Hsu, Hsien-Da Huang, Sheng-Da Hsu, Li-Zen Lin, Ann-Ping Tsou, Ching-Ping Tseng, Peter F. Stadler, Stefan Washietl, Ivo L. Hofacker:
  miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. 135-139
  Electronic Edition (link) BibTeX
• Sam Griffiths-Jones, Russell J. Grocock, Stijn van Dongen, Alex Bateman, Anton J. Enright:
  miRBase: microRNA sequences, targets and gene nomenclature. 140-144
  Electronic Edition (link) BibTeX
• Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, Janusz M. Bujnicki:
  MODOMICS: a database of RNA modification pathways. 145-149
  Electronic Edition (link) BibTeX
• Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, Runsheng Chen:
  NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. 150-152
  Electronic Edition (link) BibTeX
• A. J. Olson, N. Sheth, J. S. Lee, G. J. Hannon, R. Sachidanandam:
  RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs. 153-157
  Electronic Edition (link) BibTeX
• Laurent Lestrade, Michel J. Weber:
  snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. 158-162
  Electronic Edition (link) BibTeX
• Ebbe Sloth Andersen, Magnus Alm Rosenblad, Niels Larsen, Jesper Cairo Westergaard, Jody Burks, Iwona K. Wower, Jacek Wower, Jan Gorodkin, Tore Samuelsson, Christian Zwieb:
  The tmRDB and SRPDB resources. 163-168
  Electronic Edition (link) BibTeX
• Hans-Werner Mewes, Dmitrij Frishman, Klaus F. X. Mayer, Martin Münsterkötter, Octave Noubibou, Philipp Pagel, Thomas Rattei, Matthias Oesterheld, Andreas Ruepp, Volker Stümpflen:
  MIPS: analysis and annotation of proteins from whole genomes in 2005. 169-172
  Electronic Edition (link) BibTeX
• 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, Wolfgang Helmberg, Yuri Kapustin, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Stephen T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tugba O. Suzek, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko:
  Database resources of the National Center for Biotechnology Information. 173-180
  Electronic Edition (link) BibTeX
• Milton H. Saier Jr., Can V. Tran, Ravi D. Barabote:
  TCDB: the Transporter Classification Database for membrane transport protein analyses and information. 181-186
  Electronic Edition (link) BibTeX
• Cathy H. Wu, Rolf Apweiler, Amos Bairoch, Darren A. Natale, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Raja Mazumder, Claire O'Donovan, Nicole Redaschi, Baris E. Suzek:
  The Universal Protein Resource (UniProt): an expanding universe of protein information. 187-191
  Electronic Edition (link) BibTeX
• Jason P. Mulvenna, Conan K. L. Wang, David J. Craik:
  CyBase: a database of cyclic protein sequence and structure. 192-194
  Electronic Edition (link) BibTeX
• M. D. Shaji Kumar, M. Michael Gromiha:
  PINT: Protein-protein Interactions Thermodynamic Database. 195-198
  Electronic Edition (link) BibTeX
• Christopher P. Toseland, Helen M. McSparron, Matthew N. Davies, Darren R. Flower:
  PPD v1.0 - an integrated, web-accessible database of experimentally determined protein pK_a values. 199-203
  Electronic Edition (link) BibTeX
• M. D. Shaji Kumar, K. Abdulla Bava, M. Michael Gromiha, Ponraj Prabakaran, Koji Kitajima, Hatsuho Uedaira, Akinori Sarai:
  ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. 204-206
  Electronic Edition (link) BibTeX
• Michelle K. M. Chow, Abdullah A. Amin, Kate F. Fulton, Thushan Fernando, Lawrence Kamau, Chris Batty, Michael Louca, Storm Ho, James C. Whisstock, Stephen P. Bottomley, Ashley M. Buckle:
  The REFOLD database: a tool for the optimization of protein expression and refolding. 207-212
  Electronic Edition (link) BibTeX
• J. Lynn Fink, Rajith N. Aturaliya, Melissa J. Davis, Fasheng Zhang, Kelly Hanson, Melvena S. Teasdale, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Rohan D. Teasdale:
  LOCATE: a mouse protein subcellular localization database. 213-217
  Electronic Edition (link) BibTeX
• Anthony Kar Lun Leung, Laura Trinkle-Mulcahy, Yun Wah Lam, Jens S. Andersen, Matthias Mann, Angus I. Lamond:
  NOPdb: Nucleolar Proteome Database. 218-220
  Electronic Edition (link) BibTeX
• Rainer B. Lanz, Zeljko Jericevic, William J. Zuercher, Chris Watkins, David L. Steffen, Ronald Margolis, Neil J. McKenna:
  Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community. 221-226
  Electronic Edition (link) BibTeX
• Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Marco Pagni, Christian J. A. Sigrist:
  The PROSITE database. 227-230
  Electronic Edition (link) BibTeX
• Nicola D. Gold, Richard M. Jackson:
  SitesBase: a database for structure-based protein-ligand binding site comparisons. 231-234
  Electronic Edition (link) BibTeX
• Aaron Birkland, Golan Yona:
  BIOZON: a hub of heterogeneous biological data. 235-242
  Electronic Edition (link) BibTeX
• V. S. Gowri, O. Krishnadev, C. S. Swamy, Narayanaswamy Srinivasan:
  MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. 243-246
  Electronic Edition (link) BibTeX
• Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler, Sam Griffiths-Jones, Volker Hollich, Timo Lassmann, Simon Moxon, Mhairi Marshall, Ajay Khanna, Richard Durbin, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman:
  Pfam: clans, web tools and services. 247-251
  Electronic Edition (link) BibTeX
• Thomas Rattei, Roland Arnold, Patrick Tischler, Dominik Lindner, Volker Stümpflen, Hans-Werner Mewes:
  SIMAP: the similarity matrix of proteins. 252-256
  Electronic Edition (link) BibTeX
• Ivica Letunic, Richard R. Copley, Birgit Pils, Stefan Pinkert, Jörg Schultz, Peer Bork:
  SMART 5: domains in the context of genomes and networks. 257-260
  Electronic Edition (link) BibTeX
• Alexander A. Zamyatnin, Alexander S. Borchikov, Michail G. Vladimirov, Olga L. Voronina:
  The EROP-Moscow oligopeptide database. 261-266
  Electronic Edition (link) BibTeX
• Marco Donizelli, Marie-Ange Djite, Nicolas Le Novère:
  LGICdb: a manually curated sequence database after the genomes. 267-269
  Electronic Edition (link) BibTeX
• Neil D. Rawlings, Fraser R. Morton, Alan J. Barrett:
  MEROPS: the peptidase database. 270-272
  Electronic Edition (link) BibTeX
• Chittibabu Guda, Lipika R. Pal, Ilya N. Shindyalov:
  DMAPS: a database of multiple alignments for protein structures. 273-276
  Electronic Edition (link) BibTeX
• Zhanwen Li, Yuzhen Ye, Adam Godzik:
  Flexible Structural Neighborhood - a database of protein structural similarities and alignments. 277-280
  Electronic Edition (link) BibTeX
• Corin Yeats, Michael Maibaum, Russell L. Marsden, Mark Dibley, David Lee, Sarah Addou, Christine A. Orengo:
  Gene3D: modelling protein structure, function and evolution. 281-284
  Electronic Edition (link) BibTeX
• Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
  iMOTdb - a comprehensive collection of spatially interacting motifs in proteins. 285-286
  Electronic Edition (link) BibTeX
• Mohammed Tagari, John G. Tate, G. J. Swaminathan, Richard Newman, Avi Naim, Wim Vranken, A. Kapopoulou, A. Hussain, Joël Fillon, Kim Henrick, Samir S. Velankar:
  E-MSD: improving data deposition and structure quality. 287-290
  Electronic Edition (link) BibTeX
• Ursula Pieper, Narayanan Eswar, Fred P. Davis, Hannes Braberg, Mallur S. Madhusudhan, Andrea Rossi, Marc A. Martí-Renom, Rachel Karchin, Ben M. Webb, David Eramian, Min-Yi Shen, Libusha Kelly, Francisco Melo, Andrej Sali:
  MODBASE: a database of annotated comparative protein structure models and associated resources. 291-295
  Electronic Edition (link) BibTeX
• Samuel Flores, Nathaniel Echols, Duncan Milburn, Brandon Hespenheide, Kevin Keating, Jason Lu, Stephen Wells, Eric Z. Yu, Michael Thorpe, Mark Gerstein:
  The Database of Macromolecular Motions: new features added at the decade mark. 296-301
  Electronic Edition (link) BibTeX
• Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman:
  The RCSB PDB information portal for structural genomics. 302-305
  Electronic Edition (link) BibTeX
• Tiziana Castrignanò, Paolo D'Onorio De Meo, Domenico Cozzetto, Ivano Giuseppe Talamo, Anna Tramontano:
  The PMDB Protein Model Database. 306-309
  Electronic Edition (link) BibTeX
• Christof Winter, Andreas Henschel, Wan Kyu Kim, Michael Schroeder:
  SCOPPI: a structural classification of protein-protein interfaces. 310-314
  Electronic Edition (link) BibTeX
• Jürgen Kopp, Torsten Schwede:
  The SWISS-MODEL Repository: new features and functionalities. 315-318
  Electronic Edition (link) BibTeX
• Tina A. Eyre, Fabrice Ducluzeau, Tam P. Sneddon, Sue Povey, Elspeth A. Bruford, Michael J. Lush:
  The HUGO Gene Nomenclature Database, 2006 updates. 319-321
  Electronic Edition (link) BibTeX
• The Gene Ontology (GO) project in 2006. 322-326
  Electronic Edition (link) BibTeX
• Simon Whelan, Paul I. W. de Bakker, Emmanuel Quevillon, Nicolas Rodriguez, Nick Goldman:
  PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. 327-331
  Electronic Edition (link) BibTeX
• Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, Nikos Kyrpides:
  The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. 332-334
  Electronic Edition (link) BibTeX
• Roy R. Chaudhuri, Mark J. Pallen:
  xBASE, a collection of online databases for bacterial comparative genomics. 335-337
  Electronic Edition (link) BibTeX
• Emmanuel Perrodou, Caroline Deshayes, Jean Muller, Christine Schaeffer, Alain Van Dorsselaer, Raymond Ripp, Olivier Poch, Jean-Marc Reyrat, Odile Lecompte:
  ICDS database: interrupted CoDing sequences in prokaryotic genomes. 338-343
  Electronic Edition (link) BibTeX
• Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Greg Werner, Anu Padki, Xueling Zhao, Inna Dubchak, Philip Hugenholtz, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides:
  The integrated microbial genomes (IMG) system. 344-348
  Electronic Edition (link) BibTeX
• Ingo Paulsen, Arndt von Haeseler:
  INVHOGEN: a database of homologous invertebrate genes. 349-353
  Electronic Edition (link) BibTeX
• Minoru Kanehisa, Susumu Goto, Masahiro Hattori, Kiyoko F. Aoki-Kinoshita, Masumi Itoh, Shuichi Kawashima, Toshiaki Katayama, Michihiro Araki, Mika Hirakawa:
  From genomics to chemical genomics: new developments in KEGG. 354-357
  Electronic Edition (link) BibTeX
• Shujiro Okuda, Toshiaki Katayama, Shuichi Kawashima, Susumu Goto, Minoru Kanehisa:
  ODB: a database of operons accumulating known operons across multiple genomes. 358-362
  Electronic Edition (link) BibTeX
• Feng Chen, Aaron J. Mackey, Christian J. Stoeckert Jr., David S. Roos:
  OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. 363-368
  Electronic Edition (link) BibTeX
• Natalia Maltsev, Elizabeth M. Glass, Dinanath Sulakhe, Alexis A. Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, Mark D'Souza:
  PUMA2 - grid-based high-throughput analysis of genomes and metabolic pathways. 369-372
  Electronic Edition (link) BibTeX
• Huiquan Wang, Miroslava Kaloper, Craig J. Benham:
  SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes. 373-378
  Electronic Edition (link) BibTeX
• Sucheta Tripathy, Varun N. Pandey, Bing Fang, Fidel Salas, Brett M. Tyler:
  VMD: a community annotation database for oomycetes and microbial genomes. 379-381
  Electronic Edition (link) BibTeX
• Michael J. Adams, John F. Antoniw:
  DPVweb: a comprehensive database of plant and fungal virus genes and genomes. 382-385
  Electronic Edition (link) BibTeX
• Craig M. Shepherd, Ian A. Borelli, Gabriel Lander, Padmaja Natarajan, Vinay Siddavanahalli, Chandrajit L. Bajaj, John E. Johnson, Charles L. Brooks III, Vijay S. Reddy:
  VIPERdb: a relational database for structural virology. 386-389
  Electronic Edition (link) BibTeX
• Thierry Lombardot, Renzo Kottmann, Hauke Pfeffer, Michael Richter, Hanno Teeling, Christian Quast, Frank Oliver Glöckner:
  Megx.net - database resources for marine ecological genomics. 390-393
  Electronic Edition (link) BibTeX
• Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores, Verónica Jiménez-Jacinto, César Bonavides-Martínez, Juan Segura-Salazar, Agustino Martínez-Antonio, Julio Collado-Vides:
  RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. 394-397
  Electronic Edition (link) BibTeX
• Jian Yang, Lihong Chen, Jun Yu, Lilian Sun, Qi Jin:
  ShiBASE: an integrated database for comparative genomics of Shigella. 398-401
  Electronic Edition (link) BibTeX
• Guido Dieterich, Uwe Kärst, Elmar Fischer, Jürgen Wehland, Lothar Jänsch:
  LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species. 402-406
  Electronic Edition (link) BibTeX
• Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, Todd M. Lowe:
  The UCSC Archaeal Genome Browser. 407-410
  Electronic Edition (link) BibTeX
• Gopa R. Mishra, M. Suresh, K. Kumaran, N. Kannabiran, Shubha Suresh, P. Bala, K. Shivakumar, N. Anuradha, Raghunath Reddy, T. Madhan Raghavan, Shalini Menon, G. Hanumanthu, Malvika Gupta, Sapna Upendran, Shweta Gupta, M. Mahesh, Bincy Jacob, Pinky Mathew, Pritam Chatterjee, K. S. Arun, Salil Sharma, K. N. Chandrika, Nandan Deshpande, Kshitish Palvankar, R. Raghavnath, R. Krishnakanth, Hiren Karathia, B. Rekha, Rashmi Nayak, G. Vishnupriya, H. G. Mohan Kumar, M. Nagini, G. S. Sameer Kumar, Rojan Jose, P. Deepthi, S. Sujatha Mohan, T. K. B. Gandhi, H. C. Harsha, Krishna S. Deshpande, Malabika Sarker, T. S. Keshava Prasad, Akhilesh Pandey:
  Human protein reference database - 2006 update. 411-414
  Electronic Edition (link) BibTeX
• Alexander Mehrle, Heiko Rosenfelder, Ingo Schupp, Coral del Val, Dorit Arlt, Florian Hahne, Stephanie Bechtel, Jeremy Simpson, Oliver Hofmann, Winston Hide, Karl-Heinz Glatting, Wolfgang Huber, Rainer Pepperkok, Annemarie Poustka, Stefan Wiemann:
  The LIFEdb database in 2006. 415-418
  Electronic Edition (link) BibTeX
• Mark Heiges, Haiming Wang, Edward Robinson, Cristina Aurrecoechea, Xin Gao, Nivedita Kaluskar, Philippa Rhodes, Sammy Wang, Cong-Zhou He, Yanqi Su, John A. Miller, Eileen Kraemer, Jessica C. Kissinger:
  CryptoDB: a Cryptosporidium bioinformatics resource update. 419-422
  Electronic Edition (link) BibTeX
• Rex L. Chisholm, Pascale Gaudet, Eric M. Just, Karen E. Pilcher, Petra Fey, Sohel N. Merchant, Warren A. Kibbe:
  dictyBase, the model organism database for Dictyostelium discoideum. 423-427
  Electronic Edition (link) BibTeX
• Fernán Agüero, Wenlong Zheng, D. Brent Weatherly, Pablo N. Mendes, Jessica C. Kissinger:
  TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi. 428-431
  Electronic Edition (link) BibTeX
• David Sherman, Pascal Durrens, Florian Iragne, Emmanuelle Beyne, Macha Nikolski, Jean-Luc Souciet:
  Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. 432-435
  Electronic Edition (link) BibTeX
• Ulrich Güldener, Martin Münsterkötter, Matthias Oesterheld, Philipp Pagel, Andreas Ruepp, Hans-Werner Mewes, Volker Stümpflen:
  MPact: the MIPS protein interaction resource on yeast. 436-441
  Electronic Edition (link) BibTeX
• Jodi E. Hirschman, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Michael S. Livstone, Robert S. Nash, Julie Park, Rose Oughtred, Marek S. Skrzypek, Barry Starr, Chandra L. Theesfeld, Jennifer Williams, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Mayank K. Thanawala, Shuai Weng, Kara Dolinski, David Botstein, J. Michael Cherry:
  Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. 442-445
  Electronic Edition (link) BibTeX
• Miguel C. Teixeira, Pedro T. Monteiro, Pooja Jain, Sandra Tenreiro, Alexandra R. Fernandes, Nuno P. Mira, Marta Alenquer, Ana T. Freitas, Arlindo L. Oliveira, Isabel Sá-Correia:
  The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. 446-451
  Electronic Edition (link) BibTeX
• Kevin P. Byrne, Kenneth H. Wolfe:
  Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. 452-455
  Electronic Edition (link) BibTeX
• Ulrich Güldener, Gertrud Mannhaupt, Martin Münsterkötter, Dirk Haase, Matthias Oesterheld, Volker Stümpflen, Hans-Werner Mewes, Gerhard Adam:
  FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum. 456-458
  Electronic Edition (link) BibTeX
• Rainer Winnenburg, Thomas K. Baldwin, Martin Urban, Christopher J. Rawlings, Jacob Köhler, Kim E. Hammond-Kosack:
  PHI-base: a new database for pathogen host interactions. 459-464
  Electronic Edition (link) BibTeX
• Kamal Gajendran, Michael D. Gonzales, Andrew D. Farmer, Eric Archuleta, Joe Win, Mark E. Waugh, Sophien Kamoun:
  Phytophthora functional genomics database (PFGD): functional genomics of phytophthora-plant interactions. 465-470
  Electronic Edition (link) BibTeX
• David H. Johnson, Jun Tsao, Ming Luo, Mike Carson:
  SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans. 471-474
  Electronic Edition (link) BibTeX
• Erich M. Schwarz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis, Tristan J. Fiedler, Lisa R. Girard, Todd W. Harris, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Anthony Rogers, William Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Richard Durbin, John Spieth, Lincoln D. Stein, Paul W. Sternberg:
  WormBase: better software, richer content. 475-478
  Electronic Edition (link) BibTeX
• David Sims, Borisas Bursteinas, Qiong Gao, Marketa Zvelebil, Buzz Baum:
  FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets. 479-483
  Electronic Edition (link) BibTeX
• Gary Grumbling, Victor Strelets:
  FlyBase: anatomical data, images and queries. 484-488
  Electronic Edition (link) BibTeX
• Ian Flockhart, Matthew Booker, Amy Kiger, Michael Boutros, Susan Armknecht, Nadire Ramadan, Kris Richardson, Andrew Xu, Norbert Perrimon, Bernard Mathey-Prevot:
  FlyRNAi: the Drosophila RNAi screening center database. 489-494
  Electronic Edition (link) BibTeX
• James C. Sullivan, Joseph F. Ryan, James A. Watson, Jeramy Webb, James C. Mullikin, Daniel Rokhsar, John R. Finnerty:
  StellaBase: The Nematostella vectensis Genomics Database. 495-499
  Electronic Edition (link) BibTeX
• Nicholas A. Stover, Cynthia J. Krieger, Gail Binkley, Qing Dong, Dianna G. Fisk, Robert S. Nash, Anand Sethuraman, Shuai Weng, J. Michael Cherry:
  Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. 500-503
  Electronic Edition (link) BibTeX
• Gary D. Bader, Michael P. Cary, Chris Sander:
  Pathguide: a Pathway Resource List. 504-506
  Electronic Edition (link) BibTeX
• Dawn Cotter, Andreia Maer, Chittibabu Guda, Brian Saunders, Shankar Subramaniam:
  LMPD: LIPID MAPS proteome database. 507-510
  Electronic Edition (link) BibTeX
• Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne M. Paley, John Pick, Seung Yon Rhee, Christophe Tissier, Peifen Zhang, Peter D. Karp:
  MetaCyc: a multiorganism database of metabolic pathways and enzymes. 511-516
  Electronic Edition (link) BibTeX
• Lynda B. M. Ellis, Dave Roe, Lawrence P. Wackett:
  The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. 517-521
  Electronic Edition (link) BibTeX
• Peter Block, Christoph A. Sotriffer, Ingo Dramburg, Gerhard Klebe:
  AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB. 522-526
  Electronic Edition (link) BibTeX
• Aylwin Ng, Borisas Bursteinas, Qiong Gao, Ewan Mollison, Marketa Zvelebil:
  pSTIING: a "systems" approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. 527-534
  Electronic Edition (link) BibTeX
• Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Mike Tyers:
  BioGRID: a general repository for interaction datasets. 535-539
  Electronic Edition (link) BibTeX
• Anatolij Potapov, Ines Liebich, Jürgen Dönitz, Knut Schwarzer, Nicole Sasse, Torsten Schoeps, Torsten Crass, Edgar Wingender:
  EndoNet: an information resource about endocrine networks. 540-545
  Electronic Edition (link) BibTeX
• Mathias Krull, Susanne Pistor, Nico Voss, Alexander E. Kel, Ingmar Reuter, Deborah Kronenberg, Holger Michael, Knut Schwarzer, Anatolij Potapov, Claudia Choi, Olga V. Kel-Margoulis, Edgar Wingender:
  TRANSPATH^®: an information resource for storing and visualizing signaling pathways and their pathological aberrations. 546-551
  Electronic Edition (link) BibTeX
• Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai:
  DBTGR: a database of tunicate promoters and their regulatory elements. 552-555
  Electronic Edition (link) BibTeX
• Ewan Birney, T. Daniel Andrews, Mario Cáccamo, Yuan Chen, Laura Clarke, G. Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas Down, Richard Durbin, X. M. Fernandez-Suarez, Paul Flicek, Stefan Gräf, Martin Hammond, J. Herrero, Kevin L. Howe, V. Iyer, K. Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Felix Kokocinski, Eugene Kulesha, D. London, I. Longden, Craig Melsopp, Patrick Meidl, B. Overduin, A. Parker, Glenn Proctor, Andreas Prlic, Mark Rae, D. Rios, Seth Redmond, M. Schuster, I. Sealy, Stephen M. J. Searle, J. Severin, Guy Slater, Damian Smedley, James Smith, Arne Stabenau, Jim Stalker, S. Trevanion, Abel Ureta-Vidal, J. Vogel, S. White, Cara Woodwark, Tim J. P. Hubbard:
  Ensembl 2006. 556-561
  Electronic Edition (link) BibTeX
• Judith A. Blake, Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson:
  The Mouse Genome Database (MGD): updates and enhancements. 562-567
  Electronic Edition (link) BibTeX
• Andreas Ruepp, Octave Noubibou Doudieu, Jos van den Oever, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, Christine Skornia, Steffi Wanka, Thomas Rattei, Philipp Pagel, M. Louise Riley, Dmitrij Frishman, Dimitrij Surmeli, Igor V. Tetko, Matthias Oesterheld, Volker Stümpflen, Hans-Werner Mewes:
  The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. 568-571
  Electronic Edition (link) BibTeX
• Heng Li, Avril Coghlan, Jue Ruan, Lachlan James M. Coin, Jean-Karim Hériché, Lara Osmotherly, Ruiqiang Li, Tao Liu, Zhang Zhang, Lars Bolund, Gane Ka-Shu Wong, Wei-Mou Zheng, Paramvir Dehal, Jun Wang, Richard Durbin:
  TreeFam: a curated database of phylogenetic trees of animal gene families. 572-580
  Electronic Edition (link) BibTeX
• Judy Sprague, Leyla Bayraktaroglu, Dave Clements, Tom Conlin, David Fashena, Ken Frazer, Melissa Haendel, Douglas G. Howe, Prita Mani, Sridhar Ramachandran, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, Sierra Taylor, Ceri E. Van Slyke, Monte Westerfield:
  The Zebrafish Information Network: the zebrafish model organism database. 581-585
  Electronic Edition (link) BibTeX
• Kremena V. Star, Quingbin Song, Andy Zhu, Erwin P. Böttinger:
  QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL. 586-589
  Electronic Edition (link) BibTeX
• Angela S. Hinrichs, Donna Karolchik, Robert Baertsch, Galt P. Barber, Gill Bejerano, Hiram Clawson, Mark Diekhans, Terrence S. Furey, Rachel A. Harte, Fan Hsu, Jennifer Hillman-Jackson, Robert M. Kuhn, J. S. Pedersen, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Adam C. Siepel, Kayla E. Smith, Charles W. Sugnet, A. Sultan-Qurraie, Daryl J. Thomas, Heather Trumbower, R. J. Weber, M. Weirauch, Ann S. Zweig, David Haussler, W. James Kent:
  The UCSC Genome Browser Database: update 2006. 590-598
  Electronic Edition (link) BibTeX
• Johann Lenffer, Frank W. Nicholas, Kao Castle, Arjun Rao, Stefan Gregory, Michael Poidinger, Matthew D. Mailman, Shoba Ranganathan:
  OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI. 599-601
  Electronic Edition (link) BibTeX
• Ghazi O. Tadmouri, Mahmoud Taleb Al Ali, Sarah Al-Haj Ali, Najib Al Khaja:
  CTGA: the database for genetic disorders in Arab populations. 602-606
  Electronic Edition (link) BibTeX
• Xiaosong Wang, Haitao Zhao, Qingwen Xu, Weibo Jin, Changning Liu, Huagang Zhang, Zhibin Huang, Xinyu Zhang, Yu Zhang, Dianqi Xin, Andrew J. G. Simpson, Lloyd J. Old, Yanqun Na, Yi Zhao, Weifeng Chen:
  HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. 607-612
  Electronic Edition (link) BibTeX
• Adil Elfilali, Séverine Lair, Catia Verbeke, Philippe La Rosa, François Radvanyi, Emmanuel Barillot:
  ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. 613-616
  Electronic Edition (link) BibTeX
• Bernice R. Packer, Meredith Yeager, Laura Burdett, Robert Welch, Michael Beerman, Liqun Qi, Hugues Sicotte, Brian Staats, Mekhala Acharya, Andrew Crenshaw, Andrew Eckert, Vinita Puri, Daniela S. Gerhard, Stephen J. Chanock:
  SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. 617-621
  Electronic Edition (link) BibTeX
• Tzong-Yi Lee, Hsien-Da Huang, Jui-Hung Hung, Hsi-Yuan Huang, Yuh-Shyong Yang, Tzu-Hao Wang:
  dbPTM: an information repository of protein post-translational modification. 622-627
  Electronic Edition (link) BibTeX
• Osamu Ogasawara, Makiko Otsuji, Kouji Watanabe, Takayasu Iizuka, Takuro Tamura, Teruyoshi Hishiki, Shoko Kawamoto, Kousaku Okubo:
  BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. 628-631
  Electronic Edition (link) BibTeX
• Hideya Kawaji, Takeya Kasukawa, Shiro Fukuda, Shintaro Katayama, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki:
  CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. 632-636
  Electronic Edition (link) BibTeX
• Jeffrey H. Christiansen, Yiya Yang, Shanmugasundaram Venkataraman, Lorna Richardson, Peter Stevenson, Nicholas Burton, Richard A. Baldock, Duncan Davidson:
  EMAGE: a spatial database of gene expression patterns during mouse embryo development. 637-641
  Electronic Edition (link) BibTeX
• Alex S. Nord, Patricia J. Chang, Bruce R. Conklin, Antony V. Cox, Courtney A. Harper, Geoffrey G. Hicks, Conrad C. Huang, Susan J. Johns, Michiko Kawamoto, Songyan Liu, Elaine C. Meng, John H. Morris, Janet Rossant, Patricia Ruiz, William C. Skarnes, Philippe Soriano, William L. Stanford, Doug Stryke, Harald von Melchner, Wolfgang Wurst, Ken-ichi Yamamura, Stephen G. Young, Patricia C. Babbitt, Thomas E. Ferrin:
  The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. 642-648
  Electronic Edition (link) BibTeX
• Thomas McLaughlin, Jennifer A. Siepen, Julian Selley, Jennifer A. Lynch, King Wai Lau, Hujun Yin, Simon J. Gaskell, Simon J. Hubbard:
  PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns. 649-654
  Electronic Edition (link) BibTeX
• Frank Desiere, Eric W. Deutsch, Nichole L. King, Alexey I. Nesvizhskii, Parag Mallick, Jimmy Eng, Sharon Chen, James Eddes, Sandra N. Loevenich, Ruedi Aebersold:
  The PeptideAtlas project. 655-658
  Electronic Edition (link) BibTeX
• Philip Jones, Richard G. Côté, Lennart Martens, Antony F. Quinn, Chris F. Taylor, William Derache, Henning Hermjakob, Rolf Apweiler:
  PRIDE: a public repository of protein and peptide identifications for the proteomics community. 659-663
  Electronic Edition (link) BibTeX
• Xiaochen Bo, Shaoke Lou, Daochun Sun, Jing Yang, Shengqi Wang:
  AOBase: a database for antisense oligonucleotides selection and design. 664-667
  Electronic Edition (link) BibTeX
• David S. Wishart, Craig Knox, Anchi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, Jennifer Woolsey:
  DrugBank: a comprehensive resource for in silico drug discovery and exploration. 668-672
  Electronic Edition (link) BibTeX
• Yasushi Okuno, Jiyoon Yang, Kei Taneishi, Hiroaki Yabuuchi, Gozoh Tsujimoto:
  GLIDA: GPCR-ligand database for chemical genomic drug discovery. 673-677
  Electronic Edition (link) BibTeX
• Mathias Dunkel, Melanie Fullbeck, Stefanie Neumann, Robert Preissner:
  SuperNatural: a searchable database of available natural compounds. 678-683
  Electronic Edition (link) BibTeX
• Filip Pattyn, Piet Robbrecht, Anne De Paepe, Frank Speleman, Jo Vandesompele:
  RTPrimerDB: the real-time PCR primer and probe database, major update 2006. 684-688
  Electronic Edition (link) BibTeX
• Nicolas Le Novère, Benjamin J. Bornstein, Alexander Broicher, Mélanie Courtot, Marco Donizelli, Harish Dharuri, Lu Li, Herbert M. Sauro, Maria J. Schilstra, Bruce E. Shapiro, Jacky L. Snoep, Michael Hucka:
  BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. 689-691
  Electronic Edition (link) BibTeX
• Liying Cui, Narayanan Veeraraghavan, Alexander Richter, P. Kerr Wall, Robert K. Jansen, James Leebens-Mack, Izabela Makalowska, Claude W. dePamphilis:
  ChloroplastDB: the Chloroplast Genome Database. 692-696
  Electronic Edition (link) BibTeX
• Emmet A. O'Brien, Yue Zhang, LiuSong Yang, Eric Wang, Veronique Marie, B. Franz Lang, Gertraud Burger:
  GOBASE - a database of organelle and bacterial genome information. 697-699
  Electronic Edition (link) BibTeX
• Jochen Kohl, Ingo Paulsen, Thomas Laubach, Achim Radtke, Arndt von Haeseler:
  HvrBase++: a phylogenetic database for primate species. 700-704
  Electronic Edition (link) BibTeX
• H. Prokisch, Christophe Andreoli, U. Ahting, K. Heiss, Andreas Ruepp, C. Scharfe, Thomas Meitinger:
  MitoP2: the mitochondrial proteome database - now including mouse data. 705-711
  Electronic Edition (link) BibTeX
• Davina K. Button, Kevan M. A. Gartland, Leslie D. Ball, Louis Natanson, Jill S. Gartland, Gary D. Lyon:
  DRASTIC - INSIGHTS: querying information in a plant gene expression database. 712-716
  Electronic Edition (link) BibTeX
• Pankaj Jaiswal, Junjian Ni, Immanuel Yap, Doreen Ware, William Spooner, Ken Youens-Clark, Liya Ren, Chengzhi Liang, Wei Zhao, Kiran Ratnapu, Benjamin Faga, Payan Canaran, Molly Fogleman, Claire Hebbard, Shuly Avraham, Steven Schmidt, Terry M. Casstevens, Edward S. Buckler, Lincoln Stein, Susan McCouch:
  Gramene: a bird's eye view of cereal genomes. 717-723
  Electronic Edition (link) BibTeX
• Stefanie Hartmann, Dihui Lu, Jason Phillips, Todd J. Vision:
  Phytome: a platform for plant comparative genomics. 724-730
  Electronic Edition (link) BibTeX
• Mayumi Nakano, Kan Nobuta, Kalyan Vemaraju, Shivakundan Singh Tej, Jeremy W. Skogen, Blake C. Meyers:
  Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. 731-735
  Electronic Edition (link) BibTeX
• Gaëtan Droc, Manuel Ruiz, Pierre Larmande, A. Pereira, P. Piffanelli, Jean Benoît Morel, A. Dievart, Brigitte Courtois, Emmanuel Guiderdoni, Christophe Périn:
  OryGenesDB: a database for rice reverse genetics. 736-740
  Electronic Edition (link) BibTeX
• Hajime Ohyanagi, Tsuyoshi Tanaka, Hiroaki Sakai, Yasumasa Shigemoto, Kaori Yamaguchi, Takuya Habara, Yasuyuki Fujii, Baltazar A. Antonio, Yoshiaki Nagamura, Tadashi Imanishi, Kazuho Ikeo, Takeshi Itoh, Takashi Gojobori, Takuji Sasaki:
  The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. 741-744
  Electronic Edition (link) BibTeX
• Jianwei Zhang, Caishun Li, Changyin Wu, Lizhong Xiong, Guoxing Chen, Qifa Zhang, Shiping Wang:
  RMD: a rice mutant database for functional analysis of the rice genome. 745-748
  Electronic Edition (link) BibTeX
• Max Ingman, Ulf Gyllensten:
  mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. 749-751
  Electronic Edition (link) BibTeX
• Wei Zhao, Payan Canaran, Rebecca Jurkuta, Theresa Fulton, Jeffrey Glaubitz, Edward S. Buckler, John Doebley, Brandon Gaut, Major Goodman, Jim Holland, Stephen Kresovich, Michael D. McMullen, Lincoln Stein, Doreen Ware:
  Panzea: a database and resource for molecular and functional diversity in the maize genome. 752-757
  Electronic Edition (link) BibTeX
• Jeffry L. Shultz, Deepak Kurunam, Kay Shopinski, M. Javed Iqbal, Samreen Kazi, Kimberley Zobrist, Rabia Bashir, Satsuki Yaegashi, Nagajyothi Lavu, Ahmed J. Afzal, Charles R. Yesudas, M. Abdelmajid Kassem, Chengcang Wu, Hong Bin Zhang, Christopher D. Town, Khalid Meksem, David A. Lightfoot:
  The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. 758-765
  Electronic Edition (link) BibTeX
• Zhangjun Fei, Xuemei Tang, Rob Alba, James Giovannoni:
  Tomato Expression Database (TED): a suite of data presentation and analysis tools. 766-770
  Electronic Edition (link) BibTeX
• Agnes P. Chan, Geo Pertea, Foo Cheung, Dan Lee, Li Zheng, Cathy Whitelaw, Ana C. Pontaroli, Phillip SanMiguel, Yinan Yuan, Jeffrey Bennetzen, William Brad Barbazuk, John Quackenbush, Pablo D. Rabinowicz:
  The TIGR Maize Database. 771-776
  Electronic Edition (link) BibTeX
• Avner Schlessinger, Yanay Ofran, Guy Yachdav, Burkhard Rost:
  Epitome: database of structure-inferred antigenic epitopes. 777-780
  Electronic Edition (link) BibTeX
• Véronique Giudicelli, Patrice Duroux, Chantal Ginestoux, Géraldine Folch, Joumana Jabado-Michaloud, Denys Chaume, Marie-Paule Lefranc:
  IMGT/LIGM-DB, the IMGT^® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. 781-784
  Electronic Edition (link) BibTeX

Volume 34, Number Web-Server-Issue, 1 July 2006

• Editorial. 1
  Electronic Edition (link) BibTeX

• Joanne A. Fox, Scott McMillan, B. F. Francis Ouellette:
  A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory. 3-5
  Electronic Edition (link) BibTeX
• Jian Ye, Scott McGinnis, Thomas L. Madden:
  BLAST: improvements for better sequence analysis. 6-9
  Electronic Edition (link) BibTeX
• Jeanette Tångrot, Lixiao Wang, Bo Kågström, Uwe H. Sauer:
  FISH - family identification of sequence homologues using structure anchored hidden Markov models. 10-14
  Electronic Edition (link) BibTeX
• Markus Rampp, Thomas Soddemann, Hermann Lederer:
  The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. 15-19
  Electronic Edition (link) BibTeX
• Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, Haruki Nakamura:
  PreBI: prediction of biological interfaces of proteins in crystals. 20-24
  Electronic Edition (link) BibTeX
• Hanjo Täubig, Arno Buchner, Jan Griebsch:
  PAST: fast structure-based searching in the PDB. 20-23
  Electronic Edition (link) BibTeX
• Lee-Wei Yang, A. J. Rader, Xiong Liu, Christopher Jon Jursa, Shann-Ching Chen, Hassan A. Karimi, Ivet Bahar:
  oGNM: online computation of structural dynamics using the Gaussian Network Model. 24-31
  Electronic Edition (link) BibTeX
• Z. R. Li, H. H. Lin, L. Y. Han, L. Jiang, X. Chen, Yu Zong Chen:
  PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. 32-37
  Electronic Edition (link) BibTeX
• Cyril Azuara, Erik Lindahl, Patrice Koehl, Henri Orland, Marc Delarue:
  PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. 38-42
  Electronic Edition (link) BibTeX
• Alexander A. Kantardjiev, Boris P. Atanasov:
  PHEPS: web-based pH-dependent Protein Electrostatics Server. 43-47
  Electronic Edition (link) BibTeX
• Barbara M. Tynan-Connolly, Jens Erik Nielsen:
  pKD: re-designing protein pK_a values. 48-51
  Electronic Edition (link) BibTeX
• Erik Lindahl, Cyril Azuara, Patrice Koehl, Marc Delarue:
  NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. 52-56
  Electronic Edition (link) BibTeX
• Yunho Jang, Jay I. Jeong, Moon K. Kim:
  UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models. 57-62
  Electronic Edition (link) BibTeX
• Mark V. Berjanskii, Stephen Neal, David S. Wishart:
  PREDITOR: a web server for predicting protein torsion angle restraints. 63-69
  Electronic Edition (link) BibTeX
• M. Michael Gromiha, A. Mary Thangakani, Samuel Selvaraj:
  FOLD-RATE: prediction of protein folding rates from amino acid sequence. 70-74
  Electronic Edition (link) BibTeX
• Jean-Christophe Gelly, Catherine Etchebest, Serge A. Hazout, Alexandre G. de Brevern:
  Protein Peeling 2: a web server to convert protein structures into series of protein units. 75-78
  Electronic Edition (link) BibTeX
• Razif R. Gabdoulline, S. Ulbrich, Stefan Richter, Rebecca C. Wade:
  ProSAT2 - Protein Structure Annotation Server. 79-83
  Electronic Edition (link) BibTeX
• Rasmus Wernersson, Kristoffer Rapacki, Hans Henrik Stærfeldt, Peter Wad Sackett, Anne Mølgaard:
  FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB. 84-88
  Electronic Edition (link) BibTeX
• Jui-Hung Hung, Hsien-Da Huang, Tzong-Yi Lee:
  ProKware: integrated software for presenting protein structural properties in protein tertiary structures. 89-94
  Electronic Edition (link) BibTeX
• Edward S. C. Shih, Ruei-chi R. Gan, Ming-Jing Hwang:
  OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures. 95-98
  Electronic Edition (link) BibTeX
• Sunghoon Lee, Byungwook Lee, Insoo Jang, Sangsoo Kim, Jong Bhak:
  Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. 99-103
  Electronic Edition (link) BibTeX
• Blaise T. F. Alako, Daphne Rainey, Harm Nijveen, Jack A. M. Leunissen:
  TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure. 104-109
  Electronic Edition (link) BibTeX
• Angel Carro, Michael L. Tress, David de Juan, Florencio Pazos, Pedro Lopez-Romero, Antonio del Sol, Alfonso Valencia, Ana María Rojas:
  TreeDet: a web server to explore sequence space. 110-115
  Electronic Edition (link) BibTeX
• Joe Dundas, Zheng Ouyang, Jeffery Tseng, T. Andrew Binkowski, Yaron Turpaz, Jie Liang:
  CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. 116-118
  Electronic Edition (link) BibTeX
• M. Tyagi, P. Sharma, C. S. Swamy, F. Cadet, N. Srinivasan, Alexandre G. de Brevern, B. Offmann:
  Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. 119-123
  Electronic Edition (link) BibTeX
• Shandar Ahmad, Hidetoshi Kono, Marcos J. Araúzo-Bravo, Akinori Sarai:
  ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. 124-127
  Electronic Edition (link) BibTeX
• K. Sumathi, P. Ananthalakshmi, M. N. A. Md. Roshan, Krishna Sekar:
  3dSS: 3D structural superposition. 128-132
  Electronic Edition (link) BibTeX
• Hatice Gulcin Ozer, William C. Ray:
  MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments. 133-136
  Electronic Edition (link) BibTeX
• Johannes Söding, Michael Remmert, Andreas Biegert:
  HHrep: de novo protein repeat detection and the origin of TIM barrels. 137-142
  Electronic Edition (link) BibTeX
• R. Bhadra, S. Sandhya, K. R. Abhinandan, Saikat Chakrabarti, Ramanathan Sowdhamini, N. Srinivasan:
  Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. 143-146
  Electronic Edition (link) BibTeX
• Julien Maupetit, R. Gautier, Pierre Tufféry:
  SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. 147-151
  Electronic Edition (link) BibTeX
• Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang:
  (PS)²: protein structure prediction server. 152-157
  Electronic Edition (link) BibTeX
• Lusheng Chen, Wei Wang, Shaoping Ling, Caiyan Jia, Fei Wang:
  KemaDom: a web server for domain prediction using kernel machine with local context. 158-163
  Electronic Edition (link) BibTeX
• Alessandro Vullo, Oscar Bortolami, Gianluca Pollastri, Silvio C. E. Tosatto:
  Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. 164-168
  Electronic Edition (link) BibTeX
• Mauro Amico, Michele Finelli, Ivan Rossi, Andrea Zauli, Arne Elofsson, Håkan Viklund, Gunnar von Heijne, David Jones, Anders Krogh, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
  PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. 169-172
  Electronic Edition (link) BibTeX
• Narcis Fernandez-Fuentes, Jun Zhai, András Fiser:
  ArchPRED: a template based loop structure prediction server. 173-176
  Electronic Edition (link) BibTeX
• Alessio Ceroni, Andrea Passerini, Alessandro Vullo, Paolo Frasconi:
  DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. 177-181
  Electronic Edition (link) BibTeX
• Fabrizio Ferrè, Peter Clote:
  DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification. 182-185
  Electronic Edition (link) BibTeX
• Henry R. Bigelow, Burkhard Rost:
  PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. 186-188
  Electronic Edition (link) BibTeX
• Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert:
  transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. 189-193
  Electronic Edition (link) BibTeX
• Pierre Dönnes, Oliver Kohlbacher:
  SVMHC: a server for prediction of MHC-binding peptides. 194-197
  Electronic Edition (link) BibTeX
• Tun-Wen Pai, Margaret Dah-Tsyr Chang, Wen-Shyong Tzou, Bo-Han Su, Pei-Chih Wu, Hao-Teng Chang, Wei-I Chou:
  R_EMUS: a tool for identification of unique peptide segments as epitopes. 198-201
  Electronic Edition (link) BibTeX
• Sudipto Saha, G. P. S. Raghava:
  AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. 202-209
  Electronic Edition (link) BibTeX
• Chittibabu Guda:
  pTARGET: a web server for predicting protein subcellular localization. 210-213
  Electronic Edition (link) BibTeX
• Maria Novatchkova, Georg Schneider, Richard Fritz, Frank Eisenhaber, Alexander Schleiffer:
  DOUTfinder - identification of distant domain outliers using subsignificant sequence similarity. 214-218
  Electronic Edition (link) BibTeX
• Honglin Li, Zhenting Gao, Ling Kang, Hailei Zhang, Kun Yang, Kunqian Yu, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Jianhua Shen, Xicheng Wang, Hualiang Jiang:
  TarFisDock: a web server for identifying drug targets with docking approach. 219-224
  Electronic Edition (link) BibTeX
• Ana P. C. Rodrigues, Barry J. Grant, Roderick E. Hubbard:
  sgTarget: a target selection resource for structural genomics. 225-230
  Electronic Edition (link) BibTeX
• Ganesan Pugalenthi, K. Shameer, N. Srinivasan, Ramanathan Sowdhamini:
  HARMONY: a server for the assessment of protein structures. 231-234
  Electronic Edition (link) BibTeX
• Yi Liu, Brian Kuhlman:
  RosettaDesign server for protein design. 235-238
  Electronic Edition (link) BibTeX
• Vijaya Parthiban, M. Michael Gromiha, Dietmar Schomburg:
  CUPSAT: prediction of protein stability upon point mutations. 239-242
  Electronic Edition (link) BibTeX
• Liangjiang Wang, Susan J. Brown:
  BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. 243-248
  Electronic Edition (link) BibTeX
• Hu Chen, Yu Xue, Ni Huang, Xuebiao Yao, Zhirong Sun:
  MeMo: a web tool for prediction of protein methylation modifications. 249-253
  Electronic Edition (link) BibTeX
• Yu Xue, Fengfeng Zhou, Chuanhai Fu, Ying Xu, Xuebiao Yao:
  SUMOsp: a web server for sumoylation site prediction. 254-257
  Electronic Edition (link) BibTeX
• Sangtae Kim, Seungjin Na, Ji Woong Sim, Heejin Park, Jaeho Jeong, Hokeun Kim, Younghwan Seo, Jawon Seo, Kong-Joo Lee, Eunok Paek:
  MODⁱ : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra. 258-263
  Electronic Edition (link) BibTeX
• Nagarajan Harish, Rekha Gupta, Parul Agarwal, Vinod Scaria, Beena Pillai:
  DyNAVacS: an integrative tool for optimized DNA vaccine design. 264-266
  Electronic Edition (link) BibTeX
• Bruce R. Southey, Andinet Amare, Tyler A. Zimmerman, Sandra L. Rodriguez-Zas, Jonathan V. Sweedler:
  NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides. 267-272
  Electronic Edition (link) BibTeX
• Anne de Jong, Sacha A. F. T. van Hijum, Jetta J. E. Bijlsma, Jan Kok, Oscar P. Kuipers:
  BAGEL: a web-based bacteriocin genome mining tool. 273-279
  Electronic Edition (link) BibTeX
• Shu Ju Hsieh, Chun-Yuan Lin, Ning Han Liu, Wei Yuan Chow, Chuan Yi Tang:
  GeneAlign: a coding exon prediction tool based on phylogenetical comparisons. 280-284
  Electronic Edition (link) BibTeX
• Simona Rossi, Daniele Masotti, Christine Nardini, Elena Bonora, Giovanni Romeo, Enrico Macii, Luca Benini, Stefano Volinia:
  TOM: a web-based integrated approach for identification of candidate disease genes. 285-292
  Electronic Edition (link) BibTeX
• Jia Ye, Lin Fang, Hongkun Zheng, Yong Zhang, Jie Chen, Zengjin Zhang, Jing Wang, Shengting Li, Ruiqiang Li, Lars Bolund, Jun Wang:
  WEGO: a web tool for plotting GO annotations. 293-297
  Electronic Edition (link) BibTeX
• Carlos Prieto, Javier De Las Rivas:
  APID: Agile Protein Interaction DataAnalyzer. 298-302
  Electronic Edition (link) BibTeX
• Darby Tien-Hao Chang, Yi-Zhong Weng, Jung-Hsin Lin, Ming-Jing Hwang, Yen-Jen Oyang:
  Protemot: prediction of protein binding sites with automatically extracted geometrical templates. 303-309
  Electronic Edition (link) BibTeX
• Andrey Tovchigrechko, Ilya A. Vakser:
  GRAMM-X public web server for protein-protein docking. 310-314
  Electronic Edition (link) BibTeX
• José M. G. Izarzugaza, David de Juan, Carles Pons, Juan A. G. Ranea, Alfonso Valencia, Florencio Pazos:
  TSEMA: interactive prediction of protein pairings between interacting families. 315-319
  Electronic Edition (link) BibTeX
• Laetitia Martin, Vincent Catherinot, Gilles Labesse:
  kinDOCK: a tool for comparative docking of protein kinase ligands. 325-329
  Electronic Edition (link) BibTeX
• Christopher J. Penkett, James A. Morris, Valerie Wood, Jürg Bähler:
  YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. 330-334
  Electronic Edition (link) BibTeX
• Andreas Biegert, Christian Mayer, Michael Remmert, Johannes Söding, Andrei N. Lupas:
  The MPI Bioinformatics Toolkit for protein sequence analysis. 335-339
  Electronic Edition (link) BibTeX
• Naveed Massjouni, Corban G. Rivera, T. M. Murali:
  VIRGO: computational prediction of gene functions. 340-344
  Electronic Edition (link) BibTeX
• Chisato Yamasaki, Hiroaki Kawashima, Fusano Todokoro, Yasuhiro Imamizu, Makoto Ogawa, Motohiko Tanino, Takeshi Itoh, Takashi Gojobori, Tadashi Imanishi:
  TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB. 345-349
  Electronic Edition (link) BibTeX
• Victor Neduva, Robert B. Russell:
  DILIMOT: discovery of linear motifs in proteins. 350-355
  Electronic Edition (link) BibTeX
• Chen-Ming Hsu, Chien-Yu Chen, Baw-Jhiune Liu:
  MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences. 356-361
  Electronic Edition (link) BibTeX
• Edouard De Castro, Christian J. A. Sigrist, Alexandre Gattiker, Virginie Bulliard, Petra S. Langendijk-Genevaux, Elisabeth Gasteiger, Amos Bairoch, Nicolas Hulo:
  ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. 362-365
  Electronic Edition (link) BibTeX
• Shane Neph, Martin Tompa:
  MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. 366-368
  Electronic Edition (link) BibTeX
• Timothy L. Bailey, Nadya Williams, Chris Misleh, Wilfred W. Li:
  MEME: discovering and analyzing DNA and protein sequence motifs. 369-373
  Electronic Edition (link) BibTeX
• Johannes Söding, Michael Remmert, Andreas Biegert, Andrei N. Lupas:
  HHsenser: exhaustive transitive profile search using HMM-HMM comparison. 374-378
  Electronic Edition (link) BibTeX
• Iddo Friedberg, Tim Harder, Adam Godzik:
  JAFA: a protein function annotation meta-server. 379-381
  Electronic Edition (link) BibTeX
• Han Liang, Weihua Zhou, Laura F. Landweber:
  SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis. 382-384
  Electronic Edition (link) BibTeX
• Rasmus Wernersson:
  Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation. 385-388
  Electronic Edition (link) BibTeX
• Federico Abascal, Rafael Zardoya, David Posada:
  GenDecoder: genetic code prediction for metazoan mitochondria. 389-393
  Electronic Edition (link) BibTeX
• T. Z. DeSantis Jr., Philip Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, G. L. Andersen:
  NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. 394-399
  Electronic Edition (link) BibTeX
• Tobias Dezulian, Martin Schaefer, Roland Wiese, Detlef Weigel, Daniel H. Huson:
  CrossLink: visualization and exploration of sequence relationships between (micro) RNAs. 400-404
  Electronic Edition (link) BibTeX
• Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro:
  CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments. 405-411
  Electronic Edition (link) BibTeX
• Oranit Dror, Ruth Nussinov, Haim J. Wolfson:
  The ARTS web server for aligning RNA tertiary structures. 412-415
  Electronic Edition (link) BibTeX
• Yanga Byun, Kyungsook Han:
  PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. 416-422
  Electronic Edition (link) BibTeX
• Tzu-Hao Chang, Hsien-Da Huang, Tzu-Neng Chuang, Dray-Ming Shien, Jorng-Tzong Horng:
  RNAMST: efficient and flexible approach for identifying RNA structural homologs. 423-428
  Electronic Edition (link) BibTeX
• Hsi-Yuan Huang, Chia-Hung Chien, Kuan-Hua Jen, Hsien-Da Huang:
  RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. 429-434
  Electronic Edition (link) BibTeX
• Mario Stanke, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, Burkhard Morgenstern:
  AUGUSTUS: ab initio prediction of alternative transcripts. 435-439
  Electronic Edition (link) BibTeX
• Tiziana Castrignanò, Raffaella Rizzi, Ivano Giuseppe Talamo, Paolo D'Onorio De Meo, Anna Anselmo, Paola Bonizzoni, Graziano Pesole:
  ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization. 440-443
  Electronic Edition (link) BibTeX
• Durgaprasad Bollina, Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan:
  ASGS: an alternative splicing graph web service. 444-447
  Electronic Edition (link) BibTeX
• Yuki Naito, Kumiko Ui-Tei, Toru Nishikawa, Yutaka Takebe, Kaoru Saigo:
  siVirus: web-based antiviral siRNA design software for highly divergent viral sequences. 448-450
  Electronic Edition (link) BibTeX
• Jan Krüger, Marc Rehmsmeier:
  RNAhybrid: microRNA target prediction easy, fast and flexible. 451-454
  Electronic Edition (link) BibTeX
• Jin-Wu Nam, Jinhan Kim, Sung-Kyu Kim, Byoung-Tak Zhang:
  ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs. 455-458
  Electronic Edition (link) BibTeX
• Ali Masoudi-Nejad, Koichiro Tonomura, Shuichi Kawashima, Yuki Moriya, Masanori Suzuki, Masumi Itoh, Minoru Kanehisa, Takashi Endo, Susumu Goto:
  EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. 459-462
  Electronic Edition (link) BibTeX
• Ming Zhang, Anne-Kathrin Schultz, Charles Calef, Carla Kuiken, Thomas Leitner, Bette Korber, Burkhard Morgenstern, Mario Stanke:
  jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. 463-465
  Electronic Edition (link) BibTeX
• Michael Baitaluk, Mayya Sedova, Animesh Ray, Amarnath Gupta:
  BiologicalNetworks: visualization and analysis tool for systems biology. 466-471
  Electronic Edition (link) BibTeX
• Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, David Montaner, Eva Alloza, Juan M. Vaquerizas, Lucía Conde, Christian Blaschke, Javier Vera, Joaquín Dopazo:
  BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. 472-476
  Electronic Edition (link) BibTeX
• Stéphane Liva, Philippe Hupé, Pierre Neuvial, Isabel Brito, Eric Viara, Philippe La Rosa, Emmanuel Barillot:
  CAPweb: a bioinformatics CGH array Analysis Platform. 477-481
  Electronic Edition (link) BibTeX
• Fabrizio Ferrè, Peter Clote:
  BTW: a web server for Boltzmann time warping of gene expression time series. 482-485
  Electronic Edition (link) BibTeX
• David Montaner, Joaquín Tárraga, Jaime Huerta-Cepas, Jordi Burguet-Castell, Juan M. Vaquerizas, Lucía Conde, Pablo Minguez, Javier Vera, Sach Mukherjee, Joan Valls, Miguel A. G. Pujana, Eva Alloza, Javier Herrero, Fátima Al-Shahrour, Joaquín Dopazo:
  Next station in microarray data analysis: GEPAS. 486-491
  Electronic Edition (link) BibTeX
• Yu-Peng Wang, Liang Liang, Bu-Cong Han, Yu Quan, Xiao Wang, Tao Tao, Zhi Liang Ji:
  GEPS: the Gene Expression Pattern Scanner. 492-497
  Electronic Edition (link) BibTeX
• Johannes Rainer, Fatima Sanchez-Cabo, Gernot Stocker, Alexander Sturn, Zlatko Trajanoski:
  CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. 498-503
  Electronic Edition (link) BibTeX
• Iain W. Manfield, Chih-Hung Jen, John W. Pinney, Ioannis Michalopoulos, James R. Bradford, Philip M. Gilmartin, David R. Westhead:
  Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. 504-509
  Electronic Edition (link) BibTeX
• Maurice Scheer, Frank Klawonn, Richard Münch, Andreas Grote, Karsten Hiller, Claudia Choi, Ina Koch, Max Schobert, Elisabeth Härtig, Ulrich Klages, Dieter Jahn:
  JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. 510-515
  Electronic Edition (link) BibTeX
• Jeffrey G. Mandell, Carlos F. Barbas III:
  Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. 516-523
  Electronic Edition (link) BibTeX
• Ian John Donaldson, Berthold Göttgens:
  TFBScluster web server for the identification of mammalian composite regulatory elements. 524-528
  Electronic Edition (link) BibTeX
• Jan Grau, Irad E. Ben-Gal, Stefan Posch, Ivo Grosse:
  VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees. 529-533
  Electronic Edition (link) BibTeX
• Matti Kankainen, Petri Pehkonen, Päivi Rosenstöm, Petri Törönen, Garry Wong, Liisa Holm:
  POXO: a web-enabled tool series to discover transcription factor binding sites. 534-540
  Electronic Edition (link) BibTeX
• T. Waleev, D. Shtokalo, Tatiana Konovalova, Nico Voss, Evgeny Cheremushkin, P. Stegmaier, Olga V. Kel-Margoulis, Edgar Wingender, Alexander E. Kel:
  Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm. 541-545
  Electronic Edition (link) BibTeX
• Thomas Fiedler, Marc Rehmsmeier:
  jPREdictor: a versatile tool for the prediction of cis-regulatory elements. 546-550
  Electronic Edition (link) BibTeX
• Xuwo Ji, Wei Li, Jun Song, Liping Wei, X. Shirley Liu:
  CEAS: cis-regulatory element annotation system. 551-554
  Electronic Edition (link) BibTeX
• Saurabh Sinha, Yupu Liang, Eric D. Siggia:
  Stubb: a program for discovery and analysis of cis-regulatory modules. 555-559
  Electronic Edition (link) BibTeX
• Peter Luykx, Ivan V. Bajic, Sawsan Khuri:
  NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors. 560-565
  Electronic Edition (link) BibTeX
• Giulio Pavesi, Paolo Mereghetti, Federico Zambelli, Marco Stefani, Giancarlo Mauri, Graziano Pesole:
  MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. 566-570
  Electronic Edition (link) BibTeX
• Chun-Chi Liu, Chin-Chung Lin, Wen-Shyen E. Chen, Hsuan-Yu Chen, Pei-Chun Chang, Jeremy J. W. Chen, Pan-Chyr Yang:
  CRSD: a comprehensive web server for composite regulatory signature discovery. 571-577
  Electronic Edition (link) BibTeX
• Aurélie Lardenois, Frédéric Chalmel, Laurent Bianchetti, José-Alain Sahel, Thierry Léveillard, Olivier Poch:
  PromAn: an integrated knowledge-based web server dedicated to promoter analysis. 578-583
  Electronic Edition (link) BibTeX
• Sarita Ranjan, Jayashree Seshadri, Vaibhav Vindal, Sailu Yellaboina, Akash Ranjan:
  iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species. 584-587
  Electronic Edition (link) BibTeX
• Maike Tech, Burkhard Morgenstern, Peter Meinicke:
  TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites. 588-590
  Electronic Edition (link) BibTeX
• Igor V. Deyneko, Björn Bredohl, Daniel Wesely, Yulia M. Kalybaeva, Alexander E. Kel, Helmut Blöcker, Gerhard Kauer:
  FeatureScan: revealing property-dependent similarity of nucleotide sequences. 591-595
  Electronic Edition (link) BibTeX
• Timo Lassmann, Erik L. L. Sonnhammer:
  Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. 596-599
  Electronic Edition (link) BibTeX
• Sébastien Moretti, Frédéric Reinier, Olivier Poirot, Fabrice Armougom, Stéphane Audic, Vladimir Keduas, Cédric Notredame:
  PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. 600-603
  Electronic Edition (link) BibTeX
• Fabrice Armougom, Sébastien Moretti, Olivier Poirot, Stéphane Audic, Pierre Dumas, Basile Schaeli, Vladimir Keduas, Cédric Notredame:
  Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. 604-608
  Electronic Edition (link) BibTeX
• Mikita Suyama, David Torrents, Peer Bork:
  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. 609-612
  Electronic Edition (link) BibTeX
• Neil C. Jones, Degui Zhi, Benjamin J. Raphael:
  AliWABA: alignment on the web through an A-Bruijn approach. 613-616
  Electronic Edition (link) BibTeX
• Fei Fang, Mathieu Blanchette:
  FootPrinter3: phylogenetic footprinting in partially alignable sequences. 617-620
  Electronic Edition (link) BibTeX
• Lucía Conde, Juan M. Vaquerizas, Hernán Dopazo, Leonardo Arbiza, Joke Reumers, Frederic Rousseau, Joost Schymkowitz, Joaquín Dopazo:
  PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. 621-625
  Electronic Edition (link) BibTeX
• Purvesh Khatri, Valmik Desai, Adi L. Tarca, Sivakumar Sellamuthu, Derek E. Wildman, Roberto Romero, Sorin Draghici:
  New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. 626-631
  Electronic Edition (link) BibTeX
• Sònia Casillas, Antonio Barbadilla:
  PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA. 632-634
  Electronic Edition (link) BibTeX
• Hsiang-Yu Yuan, Jen-Jie Chiou, Wen-Hsien Tseng, Chia-Hung Liu, Chuan-Kun Liu, Yi-Jung Lin, Hui-Hung Wang, Adam Yao, Yuan-Tsong Chen, Chun-Nan Hsu:
  FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. 635-641
  Electronic Edition (link) BibTeX
• Areum Han, Hyo Jin Kang, Yoobok Cho, Sunghoon Lee, Young Joo Kim, Sungsam Gong:
  SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences. 642-644
  Electronic Edition (link) BibTeX
• Paul D. Thomas, Anish Kejariwal, Nan Guo, Huaiyu Mi, Michael J. Campbell, Anushya Muruganujan, Betty Lazareva-Ulitsky:
  Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. 645-650
  Electronic Edition (link) BibTeX
• Reidar Andreson, Tarmo Puurand, Maido Remm:
  SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. 651-655
  Electronic Edition (link) BibTeX
• Erica G. Jewell, Andrew Robinson, David Savage, Timothy A. Erwin, Christopher G. Love, Geraldine A. C. Lim, Xi Li, Jacqueline Batley, German C. Spangenberg, David Edwards:
  SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery. 656-659
  Electronic Edition (link) BibTeX
• Fengxia Yao, Ruifang Zhang, Zanhua Zhu, Kun Xia, Chunyu Liu:
  MutScreener: primer design tool for PCR-direct sequencing. 660-664
  Electronic Edition (link) BibTeX
• Tomoyuki Yamada, Haruhiko Soma, Shinichi Morishita:
  PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome. 665-669
  Electronic Edition (link) BibTeX
• Jakob Fredslund, Lene H. Madsen, Birgit K. Hougaard, Niels Sandal, Jens Stougaard, David Bertioli, Leif Schauser:
  GeMprospector - online design of cross-species genetic marker candidates in legumes and grasses. 670-675
  Electronic Edition (link) BibTeX
• Oleg Kikin, Lawrence D'Antonio, Paramjeet Bagga:
  QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. 676-682
  Electronic Edition (link) BibTeX
• Vinod Scaria, Manoj Hariharan, Amit Arora, Souvik Maiti:
  Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences. 683-685
  Electronic Edition (link) BibTeX
• Feng Gao, Chun-Ting Zhang:
  GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. 686-691
  Electronic Edition (link) BibTeX
• Philipp W. Messer, Peter F. Arndt:
  CorGen - measuring and generating long-range correlations for DNA sequence analysis. 692-695
  Electronic Edition (link) BibTeX
• Ying Chih Lin, Chin Lung Lu, Ying-Chuan Liu, Chuan Yi Tang:
  SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges. 696-699
  Electronic Edition (link) BibTeX
• David Posada:
  ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. 700-703
  Electronic Edition (link) BibTeX
• Jörg Schultz, Tobias Müller, Marco Achtziger, Philipp N. Seibel, Thomas Dandekar, Matthias Wolf:
  The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses. 704-707
  Electronic Edition (link) BibTeX
• Gábor Tóth, Gábor Deák, Endre Barta, György B. Kiss:
  PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats. 708-713
  Electronic Edition (link) BibTeX
• Luca Pireddu, Duane Szafron, Paul Lu, Russell Greiner:
  The Path-A metabolic pathway prediction web server. 714-719
  Electronic Edition (link) BibTeX
• Jianmin Wu, Xizeng Mao, Tao Cai, Jingchu Luo, Liping Wei:
  KOBAS server: a web-based platform for automated annotation and pathway identification. 720-724
  Electronic Edition (link) BibTeX
• Christopher Hyland, John W. Pinney, Glenn A. McConkey, David R. Westhead:
  metaSHARK: a WWW platform for interactive exploration of metabolic networks. 725-728
  Electronic Edition (link) BibTeX
• Duncan Hull, Katy Wolstencroft, Robert Stevens, Carole A. Goble, Matthew R. Pocock, Peter Li, Tom Oinn:
  Taverna: a tool for building and running workflows of services. 729-732
  Electronic Edition (link) BibTeX
• Alexander Loß, Roland Stenutz, Eberhard Schwarzer, Claus-Wilhelm von der Lieth:
  GlyNest and CASPER: two independent approaches to estimate ¹H and ¹³C NMR shifts of glycans available through a common web-interface. 733-737
  Electronic Edition (link) BibTeX
• Maria A. Miteva, Stephanie Violas, Matthieu Montes, David Gomez, Pierre Tufféry, Bruno O. Villoutreix:
  FAF-Drugs: free ADME/tox filtering of compound collections. 738-744
  Electronic Edition (link) BibTeX
• Alfred D. Eaton:
  HubMed: a web-based biomedical literature search interface. 745-747
  Electronic Edition (link) BibTeX
• Uma Mudunuri, Robert M. Stephens, David Bruining, David Liu, Frank J. Lebeda:
  botXminer: mining biomedical literature with a new web-based application. 748-752
  Electronic Edition (link) BibTeX