Nucleic Acids Research, Volume 34

Volume 34, Database-Issue, January 1 2006

• Alex Bateman:
  EDITORIAL. 1
  

• Michael Y. Galperin:
  The Molecular Biology Database Collection: 2006 update. 3-5
  
• Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori, Yoshio Tateno:
  DDBJ in preparation for overview of research activities behind data submissions. 6-9
  
• 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
  
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
  GenBank. 16-20
  
• Namshin Kim, Pora Kim, Seungyoon Nam, Seokmin Shin, Sanghyuk Lee:
  ChimerDB - a knowledgebase for fusion sequences. 21-24
  
• K. T. Nishant, Kumar Chetan, M. R. S. Rao:
  HUMHOT: a database of human meiotic recombination hot spots. 25-28
  
• 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
  
• Patricia Siguier, Jocelyne Pérochon, L. Lestrade, J. Mahillon, Michael Chandler:
  ISfinder: the reference centre for bacterial insertion sequences. 32-36
  
• Grant H. Jacobs, Peter A. Stockwell, Warren Tate, Chris M. Brown:
  Transterm - extended search facilities and improved integration with other databases. 37-40
  
• 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
  
• 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
  
• Dirk Holste, George Huo, Vivian Tung, Christopher B. Burge:
  HOLLYWOOD: a comparative relational database of alternative splicing. 56-62
  
• Enrique Blanco, Domènec Farré, M. Mar Albà, Xavier Messeguer, Roderic Guigó:
  ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. 63-67
  
• Gordon Robertson, Misha Bilenky, Keven 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, Bernard 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
  
• Sarah K. Kummerfeld, Sarah A. Teichmann:
  DBD: a transcription factor prediction database. 74-81
  
• Christoph D. Schmid, Rouaïda Périer, Viviane Praz, Philipp Bucher:
  EPD in its twentieth year: towards complete promoter coverage of selected model organisms. 82-85
  
• Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano:
  DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. 86-89
  
• Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi, Philipp Bucher:
  HTPSELEX - a database of high-throughput SELEX libraries for transcription factor binding sites. 90-94
  
• 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
  
• 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
  
• Xin Chen, Jian-min Wu, Klaus Hornischer, Alexander E. Kel, Edgar Wingender:
  TiProD: the Tissue-specific Promoter Database. 104-107
  
• 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, Philip Stegmaier, Birgit Lewicki-Potapov, H. Saxel, Alexander E. Kel, Edgar Wingender:
  TRANSFAC^® and its module TRANSCompel^®: transcriptional gene regulation in eukaryotes. 108-110
  
• Tala Bakheet, Bryan R. G. Williams, Khalid S. A. Khabar:
  ARED 3.0: the large and diverse AU-rich transcriptome. 111-114
  
• 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
  
• Rumen Kostadinov, Nishtha Malhotra, Manuel Viotti, Robert Shine, Lawrence D'Antonio, Paramjeet Singh Bagga:
  GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. 119-124
  
• Martin Mokrejs, Václav Vopálenský, 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
  
• 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
  
• 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
  
• Sam Griffiths-Jones, Russell J. Grocock, Stijn van Dongen, Alex Bateman, Anton J. Enright:
  miRBase: microRNA sequences, targets and gene nomenclature. 140-144
  
• Stanislaw Dunin-Horkawicz, Anna Czerwoniec, Michal J. Gajda, Marcin Feder, Henri Grosjean, Janusz M. Bujnicki:
  MODOMICS: a database of RNA modification pathways. 145-149
  
• 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
  
• Andrew J. Olson, N. Sheth, J. S. Lee, G. J. Hannon, Ravi Sachidanandam:
  RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs. 153-157
  
• Laurent Lestrade, Michel J. Weber:
  snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. 158-162
  
• 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
  
• 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
  
• 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
  
• Milton H. Saier Jr., Can V. Tran, Ravi D. Barabote:
  TCDB: the Transporter Classification Database for membrane transport protein analyses and information. 181-186
  
• 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
  
• Jason P. Mulvenna, Conan K. L. Wang, David J. Craik:
  CyBase: a database of cyclic protein sequence and structure. 192-194
  
• M. D. Shaji Kumar, M. Michael Gromiha:
  PINT: Protein-protein Interactions Thermodynamic Database. 195-198
  
• 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
  
• 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
  
• 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
  
• 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
  
• Anthony Kar Lun Leung, Laura Trinkle-Mulcahy, Yun Wah Lam, Jens S. Andersen, Matthias Mann, Angus I. Lamond:
  NOPdb: Nucleolar Proteome Database. 218-220
  
• 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
  
• 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
  
• Nicola D. Gold, Richard M. Jackson:
  SitesBase: a database for structure-based protein-ligand binding site comparisons. 231-234
  
• Aaron Birkland, Golan Yona:
  BIOZON: a hub of heterogeneous biological data. 235-242
  
• V. S. Gowri, Oruganty Krishnadev, C. S. Swamy, Narayanaswamy Srinivasan:
  MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. 243-246
  
• 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
  
• Thomas Rattei, Roland Arnold, Patrick Tischler, Dominik Lindner, Volker Stümpflen, Hans-Werner Mewes:
  SIMAP: the similarity matrix of proteins. 252-256
  
• 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
  
• Alexander A. Zamyatnin, Alexander S. Borchikov, Michail G. Vladimirov, Olga L. Voronina:
  The EROP-Moscow oligopeptide database. 261-266
  
• Marco Donizelli, Marie-Ange Djite, Nicolas Le Novère:
  LGICdb: a manually curated sequence database after the genomes. 267-269
  
• Neil D. Rawlings, Fraser R. Morton, Alan J. Barrett:
  MEROPS: the peptidase database. 270-272
  
• Chittibabu Guda, Lipika R. Pal, Ilya N. Shindyalov:
  DMAPS: a database of multiple alignments for protein structures. 273-276
  
• Zhanwen Li, Yuzhen Ye, Adam Godzik:
  Flexible Structural Neighborhood - a database of protein structural similarities and alignments. 277-280
  
• 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
  
• Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
  iMOTdb - a comprehensive collection of spatially interacting motifs in proteins. 285-286
  
• Mohammed Tagari, John G. Tate, G. J. Swaminathan, Richard H. 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
  
• 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
  
• 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
  
• 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
  
• Tiziana Castrignanò, Paolo D'Onorio De Meo, Domenico Cozzetto, Ivano Giuseppe Talamo, Anna Tramontano:
  The PMDB Protein Model Database. 306-309
  
• Christof Winter, Andreas Henschel, Wan Kyu Kim, Michael Schroeder:
  SCOPPI: a structural classification of protein-protein interfaces. 310-314
  
• Jürgen Kopp, Torsten Schwede:
  The SWISS-MODEL Repository: new features and functionalities. 315-318
  
• 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
  
• The Gene Ontology (GO) project in 2006. 322-326
  
• 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
  
• Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, Nikos Kyrpides:
  The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. 332-334
  
• Roy R. Chaudhuri, Mark J. Pallen:
  xBASE, a collection of online databases for bacterial comparative genomics. 335-337
  
• 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
  
• 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
  
• Ingo Paulsen, Arndt von Haeseler:
  INVHOGEN: a database of homologous invertebrate genes. 349-353
  
• 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
  
• Shujiro Okuda, Toshiaki Katayama, Shuichi Kawashima, Susumu Goto, Minoru Kanehisa:
  ODB: a database of operons accumulating known operons across multiple genomes. 358-362
  
• 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
  
• 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
  
• 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
  
• Sucheta Tripathy, Varun N. Pandey, Bing Fang, Fidel Salas, Brett M. Tyler:
  VMD: a community annotation database for oomycetes and microbial genomes. 379-381
  
• Michael J. Adams, John F. Antoniw:
  DPVweb: a comprehensive database of plant and fungal virus genes and genomes. 382-385
  
• 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
  
• 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
  
• 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
  
• Jian Yang, Lihong Chen, Jun Yu, Lilian Sun, Qi Jin:
  ShiBASE: an integrated database for comparative genomics of Shigella. 398-401
  
• 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
  
• Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, Todd M. Lowe:
  The UCSC Archaeal Genome Browser. 407-410
  
• 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
  
• 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
  
• Mark Heiges, Haiming Wang, Edward Robinson, Cristina Aurrecoechea, Xin Gao, Nivedita Kaluskar, Philippa Rhodes, Sammy Wang, Congzhou He, Yanqi Su, John A. Miller, Eileen Kraemer, Jessica C. Kissinger:
  CryptoDB: a Cryptosporidium bioinformatics resource update. 419-422
  
• 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
  
• 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
  
• David James 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
  
• 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
  
• 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
  
• 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
  
• Kevin P. Byrne, Kenneth H. Wolfe:
  Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. 452-455
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• Gary Grumbling, Victor Strelets:
  FlyBase: anatomical data, images and queries. 484-488
  
• 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
  
• 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
  
• 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
  
• Gary D. Bader, Michael P. Cary, Chris Sander:
  Pathguide: a Pathway Resource List. 504-506
  
• Dawn Cotter, Andreia Maer, Chittibabu Guda, Brian Saunders, Shankar Subramaniam:
  LMPD: LIPID MAPS proteome database. 507-510
  
• 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
  
• Lynda B. M. Ellis, Dave Roe, Lawrence P. Wackett:
  The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. 517-521
  
• 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
  
• 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
  
• Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Mike Tyers:
  BioGRID: a general repository for interaction datasets. 535-539
  
• 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
  
• 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
  
• 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
  
• Ewan Birney, T. Daniel Andrews, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas Down, Richard Durbin, Xosé M. Fernández-Suarez, Paul Flicek, Stefan Gräf, Martin Hammond, Javier Herrero, Kevin L. Howe, Vivek Iyer, K. Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Felix Kokocinski, Eugene Kulesha, D. London, Ian Longden, Craig Melsopp, Patrick Meidl, Bert Overduin, Anne Parker, Glenn Proctor, Andreas Prlic, Mark Rae, Daniel Rios, Seth Redmond, Michael Schuster, I. Sealy, Stephen M. J. Searle, Jessica Severin, Guy Slater, Damian Smedley, James Smith, Arne Stabenau, Jim Stalker, S. Trevanion, Abel Ureta-Vidal, Jan Vogel, Simon White, Cara Woodwark, Tim J. P. Hubbard:
  Ensembl 2006. 556-561
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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, Jakob Skou 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• Thomas McLaughlin, Jennifer A. Siepen, Julian N. 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
  
• 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
  
• 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
  
• Xiaochen Bo, Shaoke Lou, Daochun Sun, Jing Yang, Shengqi Wang:
  AOBase: a database for antisense oligonucleotides selection and design. 664-667
  
• 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
  
• Yasushi Okuno, Jiyoon Yang, Kei Taneishi, Hiroaki Yabuuchi, Gozoh Tsujimoto:
  GLIDA: GPCR-ligand database for chemical genomic drug discovery. 673-677
  
• Mathias Dunkel, Melanie Füllbeck, Stefanie Neumann, Robert Preissner:
  SuperNatural: a searchable database of available natural compounds. 678-683
  
• 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
  
• 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
  
• 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
  
• 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
  
• Jochen Kohl, Ingo Paulsen, Thomas Laubach, Achim Radtke, Arndt von Haeseler:
  HvrBase++: a phylogenetic database for primate species. 700-704
  
• Holger Prokisch, Christophe Andreoli, U. Ahting, K. Heiss, Andreas Ruepp, Curt Scharfe, Thomas Meitinger:
  MitoP2: the mitochondrial proteome database - now including mouse data. 705-711
  
• 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
  
• 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
  
• Stefanie Hartmann, Dihui Lu, Jason Phillips, Todd J. Vision:
  Phytome: a platform for plant comparative genomics. 724-730
  
• 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
  
• 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
  
• 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
  
• 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
  
• Max Ingman, Ulf Gyllensten:
  mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. 749-751
  
• 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
  
• 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
  
• Zhangjun Fei, Xuemei Tang, Rob Alba, James J. Giovannoni:
  Tomato Expression Database (TED): a suite of data presentation and analysis tools. 766-770
  
• 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
  
• Avner Schlessinger, Yanay Ofran, Guy Yachdav, Burkhard Rost:
  Epitome: database of structure-inferred antigenic epitopes. 777-780
  
• 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
  

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

• Editorial. 1
  

• 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
  
• Jian Ye, Scott McGinnis, Thomas L. Madden:
  BLAST: improvements for better sequence analysis. 6-9
  
• Jeanette Tångrot, Lixiao Wang, Bo Kågström, Uwe H. Sauer:
  FISH - family identification of sequence homologues using structure anchored hidden Markov models. 10-14
  
• Markus Rampp, Thomas Soddemann, Hermann Lederer:
  The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. 15-19
  
• Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, Haruki Nakamura:
  PreBI: prediction of biological interfaces of proteins in crystals. 20-24
  
• Hanjo Täubig, Arno Buchner, Jan Griebsch:
  PAST: fast structure-based searching in the PDB. 20-23
  
• 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
  
• Ze-Rong Li, Hong Huang 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
  
• 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
  
• Alexander A. Kantardjiev, Boris P. Atanasov:
  PHEPS: web-based pH-dependent Protein Electrostatics Server. 43-47
  
• Barbara M. Tynan-Connolly, Jens Erik Nielsen:
  pKD: re-designing protein pK_a values. 48-51
  
• 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
  
• Yunho Jang, Jay I. Jeong, Moon K. Kim:
  UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models. 57-62
  
• Mark V. Berjanskii, Stephen Neal, David S. Wishart:
  PREDITOR: a web server for predicting protein torsion angle restraints. 63-69
  
• M. Michael Gromiha, A. Mary Thangakani, Samuel Selvaraj:
  FOLD-RATE: prediction of protein folding rates from amino acid sequence. 70-74
  
• 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
  
• Razif R. Gabdoulline, S. Ulbrich, Stefan Richter, Rebecca C. Wade:
  ProSAT2 - Protein Structure Annotation Server. 79-83
  
• 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
  
• Jui-Hung Hung, Hsien-Da Huang, Tzong-Yi Lee:
  ProKware: integrated software for presenting protein structural properties in protein tertiary structures. 89-94
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• Manoj Tyagi, P. Sharma, C. S. Swamy, F. Cadet, Narayanaswamy Srinivasan, Alexandre G. de Brevern, Bernard O. Offmann:
  Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. 119-123
  
• 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
  
• K. Sumathi, P. Ananthalakshmi, M. N. A. Md. Roshan, Krishna Sekar:
  3dSS: 3D structural superposition. 128-132
  
• Hatice Gulcin Ozer, William C. Ray:
  MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments. 133-136
  
• Johannes Söding, Michael Remmert, Andreas Biegert:
  HHrep: de novo protein repeat detection and the origin of TIM barrels. 137-142
  
• Rana Bhadra, S. Sandhya, K. R. Abhinandan, Saikat Chakrabarti, Ramanathan Sowdhamini, Narayanaswamy Srinivasan:
  Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. 143-146
  
• Julien Maupetit, R. Gautier, Pierre Tufféry:
  SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. 147-151
  
• Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang:
  (PS)²: protein structure prediction server. 152-157
  
• 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
  
• 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
  
• 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
  
• Narcis Fernandez-Fuentes, Jun Zhai, András Fiser:
  ArchPRED: a template based loop structure prediction server. 173-176
  
• Alessio Ceroni, Andrea Passerini, Alessandro Vullo, Paolo Frasconi:
  DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. 177-181
  
• Fabrizio Ferrè, Peter Clote:
  DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification. 182-185
  
• Henry R. Bigelow, Burkhard Rost:
  PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. 186-188
  
• 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
  
• Pierre Dönnes, Oliver Kohlbacher:
  SVMHC: a server for prediction of MHC-binding peptides. 194-197
  
• 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
  
• Sudipto Saha, G. P. S. Raghava:
  AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. 202-209
  
• Chittibabu Guda:
  pTARGET: a web server for predicting protein subcellular localization. 210-213
  
• Maria Novatchkova, Georg Schneider, Richard Fritz, Frank Eisenhaber, Alexander Schleiffer:
  DOUTfinder - identification of distant domain outliers using subsignificant sequence similarity. 214-218
  
• 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
  
• Ana P. C. Rodrigues, Barry J. Grant, Roderick E. Hubbard:
  sgTarget: a target selection resource for structural genomics. 225-230
  
• Ganesan Pugalenthi, Khader Shameer, Narayanaswamy Srinivasan, Ramanathan Sowdhamini:
  HARMONY: a server for the assessment of protein structures. 231-234
  
• Yi Liu, Brian Kuhlman:
  RosettaDesign server for protein design. 235-238
  
• Vijaya Parthiban, M. Michael Gromiha, Dietmar Schomburg:
  CUPSAT: prediction of protein stability upon point mutations. 239-242
  
• 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
  
• Hu Chen, Yu Xue, Ni Huang, Xuebiao Yao, Zhirong Sun:
  MeMo: a web tool for prediction of protein methylation modifications. 249-253
  
• Yu Xue, Fengfeng Zhou, Chuanhai Fu, Ying Xu, Xuebiao Yao:
  SUMOsp: a web server for sumoylation site prediction. 254-257
  
• 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
  
• Nagarajan Harish, Rekha Gupta, Parul Agarwal, Vinod Scaria, Beena Pillai:
  DyNAVacS: an integrative tool for optimized DNA vaccine design. 264-266
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• Carlos Prieto, Javier De Las Rivas:
  APID: Agile Protein Interaction DataAnalyzer. 298-302
  
• 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
  
• Andrey Tovchigrechko, Ilya A. Vakser:
  GRAMM-X public web server for protein-protein docking. 310-314
  
• 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
  
• Laetitia Martin, Vincent Catherinot, Gilles Labesse:
  kinDOCK: a tool for comparative docking of protein kinase ligands. 325-329
  
• 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
  
• Andreas Biegert, Christian Mayer, Michael Remmert, Johannes Söding, Andrei N. Lupas:
  The MPI Bioinformatics Toolkit for protein sequence analysis. 335-339
  
• Naveed Massjouni, Corban G. Rivera, T. M. Murali:
  VIRGO: computational prediction of gene functions. 340-344
  
• 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
  
• Victor Neduva, Robert B. Russell:
  DILIMOT: discovery of linear motifs in proteins. 350-355
  
• 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
  
• 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
  
• Shane Neph, Martin Tompa:
  MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. 366-368
  
• Timothy L. Bailey, Nadya Williams, Chris Misleh, Wilfred W. Li:
  MEME: discovering and analyzing DNA and protein sequence motifs. 369-373
  
• Johannes Söding, Michael Remmert, Andreas Biegert, Andrei N. Lupas:
  HHsenser: exhaustive transitive profile search using HMM-HMM comparison. 374-378
  
• Iddo Friedberg, Tim Harder, Adam Godzik:
  JAFA: a protein function annotation meta-server. 379-381
  
• 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
  
• Rasmus Wernersson:
  Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation. 385-388
  
• Federico Abascal, Rafael Zardoya, David Posada:
  GenDecoder: genetic code prediction for metazoan mitochondria. 389-393
  
• T. Z. DeSantis Jr., Philip Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, Gary L. Andersen:
  NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. 394-399
  
• Tobias Dezulian, Martin Schaefer, Roland Wiese, Detlef Weigel, Daniel H. Huson:
  CrossLink: visualization and exploration of sequence relationships between (micro) RNAs. 400-404
  
• Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro:
  CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments. 405-411
  
• Oranit Dror, Ruth Nussinov, Haim J. Wolfson:
  The ARTS web server for aligning RNA tertiary structures. 412-415
  
• Yanga Byun, Kyungsook Han:
  PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. 416-422
  
• 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
  
• 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
  
• Mario Stanke, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, Burkhard Morgenstern:
  AUGUSTUS: ab initio prediction of alternative transcripts. 435-439
  
• 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
  
• Durgaprasad Bollina, Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan:
  ASGS: an alternative splicing graph web service. 444-447
  
• 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
  
• Jan Krüger, Marc Rehmsmeier:
  RNAhybrid: microRNA target prediction easy, fast and flexible. 451-454
  
• 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
  
• 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
  
• Ming Zhang, Anne-Kathrin Schultz, Charles Calef, Carla Kuiken, Thomas Leitner, Bette T. Korber, Burkhard Morgenstern, Mario Stanke:
  jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. 463-465
  
• Michael Baitaluk, Mayya Sedova, Animesh Ray, Amarnath Gupta:
  BiologicalNetworks: visualization and analysis tool for systems biology. 466-471
  
• 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
  
• Stéphane Liva, Philippe Hupé, Pierre Neuvial, Isabel Brito, Eric Viara, Philippe La Rosa, Emmanuel Barillot:
  CAPweb: a bioinformatics CGH array Analysis Platform. 477-481
  
• Fabrizio Ferrè, Peter Clote:
  BTW: a web server for Boltzmann time warping of gene expression time series. 482-485
  
• 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
  
• 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
  
• 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
  
• 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
  
• 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
  
• Jeffrey G. Mandell, Carlos F. Barbas III:
  Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. 516-523
  
• Ian John Donaldson, Berthold Göttgens:
  TFBScluster web server for the identification of mammalian composite regulatory elements. 524-528
  
• Jan Grau, Irad E. Ben-Gal, Stefan Posch, Ivo Grosse:
  VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees. 529-533
  
• Matti Kankainen, Petri Pehkonen, Päivi Rosenström, Petri Törönen, Garry Wong, Liisa Holm:
  POXO: a web-enabled tool series to discover transcription factor binding sites. 534-540
  
• T. Waleev, D. Shtokalo, Tatiana Konovalova, Nico Voss, Evgeny Cheremushkin, Philip 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
  
• Thomas Fiedler, Marc Rehmsmeier:
  jPREdictor: a versatile tool for the prediction of cis-regulatory elements. 546-550
  
• Xuwo Ji, Wei Li, Jun Song, Liping Wei, X. Shirley Liu:
  CEAS: cis-regulatory element annotation system. 551-554
  
• Saurabh Sinha, Yupu Liang, Eric D. Siggia:
  Stubb: a program for discovery and analysis of cis-regulatory modules. 555-559
  
• Peter Luykx, Ivan V. Bajic, Sawsan Khuri:
  NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors. 560-565
  
• 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
  
• 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
  
• 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
  
• 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
  
• Maike Tech, Burkhard Morgenstern, Peter Meinicke:
  TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites. 588-590
  
• 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
  
• Timo Lassmann, Erik L. L. Sonnhammer:
  Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. 596-599
  
• 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
  
• 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
  
• Mikita Suyama, David Torrents, Peer Bork:
  PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. 609-612
  
• Neil C. Jones, Degui Zhi, Benjamin J. Raphael:
  AliWABA: alignment on the web through an A-Bruijn approach. 613-616
  
• Fei Fang, Mathieu Blanchette:
  FootPrinter3: phylogenetic footprinting in partially alignable sequences. 617-620
  
• 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
  
• 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
  
• Sònia Casillas, Antonio Barbadilla:
  PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA. 632-634
  
• 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
  
• 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
  
• 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
  
• Reidar Andreson, Tarmo Puurand, Maido Remm:
  SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. 651-655
  
• 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
  
• Fengxia Yao, Ruifang Zhang, Zanhua Zhu, Kun Xia, Chunyu Liu:
  MutScreener: primer design tool for PCR-direct sequencing. 660-664
  
• Tomoyuki Yamada, Haruhiko Soma, Shinichi Morishita:
  PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome. 665-669
  
• 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
  
• Oleg Kikin, Lawrence D'Antonio, Paramjeet Singh Bagga:
  QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. 676-682
  
• Vinod Scaria, Manoj Hariharan, Amit Arora, Souvik Maiti:
  Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences. 683-685
  
• 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
  
• Philipp W. Messer, Peter F. Arndt:
  CorGen - measuring and generating long-range correlations for DNA sequence analysis. 692-695
  
• 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
  
• David Posada:
  ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. 700-703
  
• 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
  
• Gábor Tóth, Gábor Deák, Endre Barta, György B. Kiss:
  PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats. 708-713
  
• Luca Pireddu, Duane Szafron, Paul Lu, Russell Greiner:
  The Path-A metabolic pathway prediction web server. 714-719
  
• Jianmin Wu, Xizeng Mao, Tao Cai, Jingchu Luo, Liping Wei:
  KOBAS server: a web-based platform for automated annotation and pathway identification. 720-724
  
• Christopher Hyland, John W. Pinney, Glenn A. McConkey, David R. Westhead:
  metaSHARK: a WWW platform for interactive exploration of metabolic networks. 725-728
  
• 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
  
• 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
  
• 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
  
• Alfred D. Eaton:
  HubMed: a web-based biomedical literature search interface. 745-747
  
• Uma Mudunuri, Robert M. Stephens, David Bruining, David Liu, Frank J. Lebeda:
  botXminer: mining biomedical literature with a new web-based application. 748-752
  

Last update Mon May 20 18:15:12 2013 CET by the DBLP Team — Data released under the ODC-BY 1.0 license — See also our legal information page