Nucleic Acids Research, Volume 33

Volume 33, Database-Issue, January 1 2005

• Alex Bateman:
  Editorial. 1
  
• Dov Greenbaum, Andrew K. Smith, Mark Gerstein:
  Editorial. 3-4
  

• Michael Y. Galperin:
  The Molecular Biology Database Collection: 2005 update. 5-24
  
• Yoshio Tateno, Naruya Saitou, Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori:
  DDBJ in collaboration with mass-sequencing teams on annotation. 25-28
  
• Carola Kanz, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Alastair Baldwin, Kirsty Bates, Paul Browne, Alexandra van den Broek, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Eberhardt, Nadeem Faruque, John Gamble, Federico Garcia Diez, Nicola Harte, Tamara Kulikova, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Siamak Sobhany, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler:
  The EMBL Nucleotide Sequence Database. 29-33
  
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
  GenBank. 34-38
  
• David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Wolfgang Helmberg, David L. Kenton, Oleg Khovayko, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Joan U. Pontius, Kim D. Pruitt, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Grigory Starchenko, Tugba O. Suzek, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko:
  Database resources of the National Center for Biotechnology Information. 39-45
  
• Catherine Brooksbank, Graham Cameron, Janet M. Thornton:
  The European Bioinformatics Institute's data resources: towards systems biology. 46-53
  
• Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova:
  Entrez Gene: gene-centered information at NCBI. 54-58
  
• Adel Khelifi, Laurent Duret, Dominique Mouchiroud:
  HOPPSIGEN: a database of human and mouse processed pseudogenes. 59-66
  
• Victor G. Levitsky, Aleksey V. Katokhin, Olga A. Podkolodnaya, Dagmara P. Furman, Nikolay A. Kolchanov:
  NPRD: Nucleosome Positioning Region Database. 67-70
  
• Yuandan Lee, Jennifer Tsai, S. Sunkara, Svetlana Karamycheva, Geo Pertea, Razvan Sultana, Valentin Antonescu, Agnes P. Chan, Foo Cheung, John Quackenbush:
  The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. 71-74
  
• Pora Kim, Namshin Kim, Younghee Lee, Bumjin Kim, Youngah Shin, Sanghyuk Lee:
  ECgene: genome annotation for alternative splicing. 75-79
  
• Hsien-Da Huang, Jorng-Tzong Horng, Feng-Mao Lin, Yu-Chung Chang, Chen-Chia Huang:
  SpliceInfo: an information repository for mRNA alternative splicing in human genome. 80-85
  
• Endre Barta, Endre Sebestyén, Tamás B. Pálfy, Gábor Tóth, Csaba P. Ortutay, László Patthy:
  DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. 86-90
  
• Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva:
  The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. 91-97
  
• Abel D. González, Vladimir Espinosa Angarica, Ana Tereza R. Vasconcelos, Ernesto Pérez-Rueda, Julio Collado-Vides:
  TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes. 98-102
  
• Fang Zhao, Zhenyu Xuan, Lihua Liu, Michael Q. Zhang:
  TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. 103-107
  
• Matthias Truss, Maciej Swat, Szymon M. Kielbasa, Reinhold Schäfer, Hanspeter Herzel, Christian Hagemeier:
  HuSiDa - the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. 108-111
  
• Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, Runsheng Chen:
  NONCODE: an integrated knowledge database of non-coding RNAs. 112-115
  
• Haibo Zhang, Jun Hu, Michael Recce, Bin Tian:
  PolyA_DB: a database for mammalian mRNA polyadenylation. 116-120
  
• Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, Alex Bateman:
  Rfam: annotating non-coding RNAs in complete genomes. 121-124
  
• Ken C. Pang, Stuart Stephen, Pär G. Engström, Khairina Tajul-Arifin, Weisan Chen, Claes Wahlestedt, Boris Lenhard, Yoshihide Hayashizaki, John S. Mattick:
  RNAdb - a comprehensive mammalian noncoding RNA database. 125-130
  
• Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer:
  siRNAdb: a database of siRNA sequences. 131-134
  
• James A. McCloskey, Jef Rozenski:
  The Small Subunit rRNA Modification Database. 135-138
  
• Mathias Sprinzl, Konstantin S. Vassilenko:
  Compilation of tRNA sequences and sequences of tRNA genes. 139-140
  
• Flavio Mignone, Giorgio Grillo, Flavio Licciulli, Michele Iacono, Sabino Liuni, Paul Kersey, Jorge Duarte, Cecilia Saccone, Graziano Pesole:
  UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. 141-146
  
• Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, Brett Poulin, Roman Eisner, Danny Ngo, Nicholas Lamb:
  PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. 147-153
  
• Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L. Yeh:
  The Universal Protein Resource (UniProt). 154-159
  
• Sven Mika, Burkhard Rost:
  NMPdb: Database of Nuclear Matrix Proteins. 160-163
  
• Sébastien Rey, Michael Acab, Jennifer L. Gardy, Matthew R. Laird, Katalin de Fays, Christophe G. Lambert, Fiona S. L. Brinkman:
  PSORTdb: a protein subcellular localization database for bacteria. 164-168
  
• Yunjia Chen, Yong Zhang, Yanbin Yin, Ge Gao, Songgang Li, Ying Jiang, Xiaocheng Gu, Jingchu Luo:
  SPD - a web-based secreted protein database. 169-173
  
• Ya-Hui Chang, Wen-Hui Su, Tso-Ching Lee, Hsiao-Fang Sunny Sun, Chia-Hsiang Chen, Wen-Harn Pan, Shih-Feng Tsai, Yuh-Shan Jou:
  TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations. 174-177
  
• Qiaojuan Jane Su, Lin Lu, Serge Saxonov, Douglas L. Brutlag:
  eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. 178-182
  
• Vladimir A. Ivanisenko, Sergey S. Pintus, Dmitry A. Grigorovich, Nikolay A. Kolchanov:
  PDBSite: a database of the 3D structure of protein functional sites. 183-187
  
• Andreas Heger, Christopher Andrew Wilton, Ashwin Sivakumar, Liisa Holm:
  ADDA: a domain database with global coverage of the protein universe. 188-191
  
• Aron Marchler-Bauer, John B. Anderson, Praveen F. Cherukuri, Carol DeWeese-Scott, Lewis Y. Geer, Marc Gwadz, Siqian He, David I. Hurwitz, John D. Jackson, Zhaoxi Ke, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Fu Lu, Gabriele H. Marchler, Mikhail Mullokandov, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Jodie J. Yin, Dachuan Zhang, Stephen H. Bryant:
  CDD: a Conserved Domain Database for protein classification. 192-196
  
• Saraswathi Abhiman, Erik L. L. Sonnhammer:
  FunShift: a database of function shift analysis on protein subfamilies. 197-200
  
• Nicola J. Mulder, Rolf Apweiler, Teresa K. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex Mitchell, Anastasia N. Nikolskaya, Sandra E. Orchard, Marco Pagni, Chris P. Ponting, Emmanuel Quevillon, Jeremy D. Selengut, Christian J. A. Sigrist, Ville Silventoinen, David J. Studholme, Robert Vaughan, Cathy H. Wu:
  InterPro, progress and status in 2005. 201-205
  
• Shu-Hsien Sheu, David R. Lancia Jr., Karl H. Clodfelter, Melissa R. Landon, Sandor Vajda:
  PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes. 206-211
  
• Catherine Bru, Emmanuel Courcelle, Sébastien Carrère, Yoann Beausse, Sandrine Dalmar, Daniel Kahn:
  The ProDom database of protein domain families: more emphasis on 3D. 212-215
  
• Noam Kaplan, Ori Sasson, Uri Inbar, Moriah Friedlich, Menachem Fromer, Hillel Fleischer, Elon Portugaly, Nathan Linial, Michal Linial:
  ProtoNet 4.0: A hierarchical classification of one million protein sequences. 216-218
  
• James A. Casbon, Mansoor A. S. Saqi:
  S4: structure-based sequence alignments of SCOP superfamilies. 219-222
  
• Kristian Vlahovicek, László Kaján, Vilmos Ágoston, Sándor Pongor:
  The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. 223-225
  
• Thomas Meinel, Antje Krause, Hannes Luz, Martin Vingron, Eike Staub:
  The SYSTERS Protein Family Database in 2005. 226-229
  
• Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
  REBASE - restriction enzymes and DNA methyltransferases. 230-232
  
• Nita Deshpande, Kenneth J. Addess, Wolfgang Bluhm, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L. Flippen-Anderson, John D. Westbrook, Helen M. Berman, Philip E. Bourne:
  The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. 233-237
  
• Jae-Min Shin, Doo-Ho Cho:
  PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures. 238-241
  
• Thomas Lütteke, Martin Frank, Claus-Wilhelm von der Lieth:
  Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. 242-246
  
• Frances M. G. Pearl, Annabel E. Todd, Ian Sillitoe, Mark Dibley, Oliver Redfern, Tony E. Lewis, Christopher Bennett, Russell L. Marsden, Alastair Grant, David Lee, Adrian Akpor, Michael Maibaum, Andrew P. Harrison, Timothy Dallman, Gabrielle A. Reeves, Ilhem Diboun, Sarah Addou, Stefano Lise, Caroline E. Johnston, Antonio Sillero, Janet M. Thornton, Christine A. Orengo:
  The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. 247-251
  
• Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
  GenDiS: Genomic Distribution of protein structural domain Superfamilies. 252-255
  
• Véronique Giudicelli, Denys Chaume, Marie-Paule Lefranc:
  IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. 256-261
  
• Samir S. Velankar, P. McNeil, Virginie Mittard-Runte, A. Suarez, Daniel Barrell, Rolf Apweiler, Kim Henrick:
  E-MSD: an integrated data resource for bioinformatics. 262-265
  
• Roman A. Laskowski, Victor V. Chistyakov, Janet M. Thornton:
  PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. 266-268
  
• Goran Neshich, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Ivan P. Pinto, Juliana F. Palandrani, João N. Krauchenco, Christian Baudet, Arnaldo J. Montagner, Roberto H. Higa:
  STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. 269-274
  
• Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon:
  PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. 275-278
  
• Kate F. Fulton, Glyn L. Devlin, Rachel A. Jodun, Linda Silvestri, Stephen P. Bottomley, Alan R. Fersht, Ashley M. Buckle:
  PFD: a database for the investigation of protein folding kinetics and stability. 279-283
  
• Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody A. Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano, Paul D. Thomas:
  The PANTHER database of protein families, subfamilies, functions and pathways. 284-288
  
• Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, Russ B. Altman:
  Biomedical term mapping databases. 289-293
  
• James R. Cole, B. Chai, Ryan J. Farris, Q. Wang, S. A. Kulam, D. M. McGarrell, George M. Garrity, James M. Tiedje:
  The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. 294-296
  
• Paul Kersey, Lawrence Bower, Lorna Morris, Alan Horne, Robert Petryszak, Carola Kanz, Alexander Kanapin, Ujjwal Das, Karine Michoud, Isabelle Phan, Alexandre Gattiker, Tamara Kulikova, Nadeem Faruque, Karyn Duggan, Peter Mclaren, Britt Reimholz, Laurent Duret, Simon Penel, Ingmar Reuter, Rolf Apweiler:
  Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. 297-302
  
• José M. Peregrin-Alvarez, Andrew Yam, Gaya Sivakumar, John Parkinson:
  PartiGeneDB - collating partial genomes. 303-307
  
• M. Louise Riley, Thorsten Schmidt, Christian Wagner, Hans-Werner Mewes, Dmitrij Frishman:
  The PEDANT genome database in 2005. 308-310
  
• Elliot J. Lefkowitz, Chris Upton, Shankar S. Changayil, Charles Buck, Paula Traktman, R. Mark L. Buller:
  Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource. 311-316
  
• Paul Stothard, Gary H. Van Domselaar, Savita Shrivastava, Anchi Guo, Brian O'Neill, Joseph A. Cruz, Michael Ellison, David S. Wishart:
  BacMap: an interactive picture atlas of annotated bacterial genomes. 317-320
  
• Hiroyuki Ogata, Jean-Michel Claverie:
  Metagrowth: a new resource for the building of metabolic hypotheses in microbiology. 321-324
  
• Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, Qi Jin:
  VFDB: a reference database for bacterial virulence factors. 325-328
  
• Raju V. Misra, Richard S. P. Horler, Wolfgang Reindl, Igor Goryanin, Gavin H. Thomas:
  EchoBASE: an integrated post-genomic database for Escherichia coli. 329-333
  
• Ingrid M. Keseler, Julio Collado-Vides, Socorro Gama-Castro, John Ingraham, Suzanne M. Paley, Ian T. Paulsen, Martín Peralta-Gil, Peter D. Karp:
  EcoCyc: a comprehensive database resource for Escherichia coli. 334-337
  
• Geoffrey L. Winsor, Raymond Lo, Shannan J. Ho Sui, Korine S. E. Ung, Shao-Shan Huang, Dean Cheng, Wai-Kay Ho Ching, Robert E. W. Hancock, Fiona S. L. Brinkman:
  Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. 338-343
  
• Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy, K. R. Rajyashri, Villoo Morawala Patell, Chris Bowler:
  The Diatom EST Database. 344-347
  
• Leandro Hermida, Sophie Brachat, Sylvia Voegeli, Peter Philippsen, Michael Primig:
  The Ashbya Genome Database (AGD) - a tool for the yeast community and genome biologists. 348-352
  
• C. d'Enfert, S. Goyard, S. Rodriguez-Arnaveilhe, L. Frangeul, L. Jones, Fredj Tekaia, O. Bader, Antje Albrecht, L. Castillo, A. Dominguez, J. F. Ernst, C. Fradin, C. Gaillardin, S. Garcia-Sanchez, P. de Groot, B. Hube, F. M. Klis, S. Krishnamurthy, D. Kunze, M.-C. Lopez, A. Mavor, N. Martin, I. Moszer, D. Onésime, J. Perez Martin, R. Sentandreu, E. Valentin, A. J. P. Brown:
  CandidaDB: a genome database for Candida albicans pathogenomics. 353-357
  
• Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Gail Binkley, Christopher Lane, Stuart R. Miyasato, Gavin Sherlock:
  The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information. 358-363
  
• Ulrich Güldener, Martin Münsterkötter, Gabi Kastenmüller, Normann Strack, Jacques van Helden, Christian Lemer, J. Richelles, Shoshana J. Wodak, J. García-Martínez, J. E. Pérez-Ortín, Holger Michael, Andreas Kaps, E. Talla, Bernard Dujon, Bruno André, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, Hans-Werner Mewes:
  CYGD: the Comprehensive Yeast Genome Database. 364-368
  
• Luciano Fernandez-Ricaud, Jonas Warringer, Elke Ericson, Ilona Pylvänäinen, Graham J. L. Kemp, Olle Nerman, Anders Blomberg:
  PROPHECY - a database for high-resolution phenomics. 369-373
  
• Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Anand Sethuraman, Shuai Weng, David Botstein, J. Michael Cherry:
  Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). 374-377
  
• Michael Riffle, Lars Malmström, Trisha N. Davis:
  The Yeast Resource Center Public Data Repository. 378-382
  
• Nansheng Chen, Todd W. Harris, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Payan Canaran, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Fiona Cunningham, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, Shraddha Pai, Philip Ozersky, Andrei Petcherski, Anthony Rogers, Aniko Sabo, Erich M. Schwarz, Kimberly Van Auken, Qinghua Wang, Richard Durbin, John Spieth, Paul W. Sternberg, Lincoln D. Stein:
  WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. 383-389
  
• Rachel A. Drysdale, Madeline A. Crosby:
  FlyBase: genes and gene models. 390-395
  
• Andre R. O. Cavalcanti, Thomas H. Clarke, Laura F. Landweber:
  MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates. 396-398
  
• Jing Wang, Qingyou Xia, Ximiao He, Mingtao Dai, Jue Ruan, Jie Chen, Guo Yu, Haifeng Yuan, Yafeng Hu, Ruiqiang Li, Tao Feng, Chen Ye, Cheng Lu, Jun Wang, Songgang Li, Gane Ka-Shu Wong, Huanming Yang, Jian Wang, Zhonghuai Xiang, Zeyang Zhou, Jun Yu:
  SilkDB: a knowledgebase for silkworm biology and genomics. 399-402
  
• M. D. Prasad, M. Muthulakshmi, K. P. Arunkumar, M. Madhu, Vattipally B. Sreenu, V. Pavithra, Buddhaditta Bose, Hampapathalu A. Nagarajaram, K. Mita, T. Shimada, Javaregowda Nagaraju:
  SilkSatDb: a microsatellite database of the silkworm, Bombyx mori. 403-406
  
• Nozomi Nagano:
  EzCatDB: the Enzyme Catalytic-mechanism Database. 407-412
  
• Amelie Stein, Robert B. Russell, Patrick Aloy:
  3did: interacting protein domains of known three-dimensional structure. 413-417
  
• C. Alfarano, C. E. Andrade, K. Anthony, N. Bahroos, M. Bajec, K. Bantoft, Doron Betel, B. Bobechko, K. Boutilier, E. Burgess, K. Buzadzija, R. Cavero, C. D'Abreo, Ian Donaldson, D. Dorairajoo, M. J. Dumontier, M. R. Dumontier, V. Earles, R. Farrall, Howard J. Feldman, E. Garderman, Y. Gong, R. Gonzaga, V. Grytsan, E. Gryz, V. Gu, E. Haldorsen, A. Halupa, R. Haw, A. Hrvojic, L. Hurrell, Ruth Isserlin, F. Jack, F. Juma, A. Khan, T. Kon, S. Konopinsky, V. Le, E. Lee, S. Ling, M. Magidin, J. Moniakis, J. Montojo, S. Moore, B. Muskat, I. Ng, J. P. Paraiso, B. Parker, Greg Pintilie, R. Pirone, John J. Salama, S. Sgro, T. Shan, Y. Shu, J. Siew, D. Skinner, Kevin A. Snyder, R. Stasiuk, D. Strumpf, Brigitte Tuekam, S. Tao, Z. Wang, M. White, R. Willis, Cheryl Wolting, S. Wong, A. Wrong, C. Xin, R. Yao, B. Yates, S. Zhang, K. Zheng, Tony Pawson, B. F. Francis Ouellette, Christopher W. V. Hogue:
  The Biomolecular Interaction Network Database and related tools 2005 update. 418-424
  
• Elena A. Ananko, Nikolay L. Podkolodny, Irina L. Stepanenko, Olga A. Podkolodnaya, D. A. Rasskazov, D. S. Miginsky, Vitali A. Likhoshvai, Alexander V. Ratushny, N. N. Podkolodnaya, Nikolay A. Kolchanov:
  GeneNet in 2005. 425-427
  
• G. Joshi-Tope, Marc Gillespie, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Bernard de Bono, Bijay Jassal, G. R. Gopinath, G. R. Wu, Lisa Matthews, Suzanna Lewis, Ewan Birney, Lincoln Stein:
  Reactome: a knowledgebase of biological pathways. 428-432
  
• Christian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork:
  STRING: known and predicted protein-protein associations, integrated and transferred across organisms. 433-437
  
• Jing Wang, Ximiao He, Jue Ruan, Mingtao Dai, Jie Chen, Yong Zhang, Yafeng Hu, Chen Ye, Shengting Li, Lijuan Cong, Lin Fang, Bin Liu, Songgang Li, Jian Wang, David W. Burt, Gane Ka-Shu Wong, Jun Yu, Huanming Yang, Jun Wang:
  ChickVD: a sequence variation database for the chicken genome. 438-441
  
• Vamsi Veeramachaneni, Wojciech Makalowski:
  DED: Database of Evolutionary Distances. 442-446
  
• Tim J. P. Hubbard, D. Andrews, Mario Cáccamo, Graham Cameron, Yuan Chen, Michele E. Clamp, Laura Clarke, G. Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas Down, Richard Durbin, X. M. Fernandez-Suarez, James Gilbert, Martin Hammond, Javier Herrero, H. Hotz, Kevin L. Howe, V. Iyer, K. Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, S. Keenan, Felix Kokocinski, D. London, I. Longden, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Simon C. Potter, Glenn Proctor, Mark Rae, D. Rios, M. Schuster, Stephen M. J. Searle, J. Severin, Guy Slater, Damian Smedley, James Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, S. Trevanion, Abel Ureta-Vidal, J. Vogel, S. White, Cara Woodwark, Ewan Birney:
  Ensembl 2005. 447-453
  
• Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, W. James Kent:
  The UCSC Proteome Browser. 454-458
  
• J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, Patrick Meidl, Stephen M. J. Searle, Jim Stalker, R. Storey, S. Trevanion, L. G. Wilming, Tim J. P. Hubbard:
  The Vertebrate Genome Annotation (Vega) database. 459-465
  
• Laura Elnitski, Belinda Giardine, Prachi Shah, Yi Zhang, Cathy Riemer, Matthew Weirauch, Richard Burhans, Webb Miller, Ross C. Hardison:
  Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. 466-470
  
• Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake:
  The Mouse Genome Database (MGD): from genes to mice - a community resource for mouse biology. 471-475
  
• Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer:
  Inparanoid: a comprehensive database of eukaryotic orthologs. 476-480
  
• Eric Bazin, Laurent Duret, Simon Penel, Nicolas Galtier:
  Polymorphix: a sequence polymorphism database. 481-484
  
• Norberto de la Cruz, Susan Bromberg, Dean Pasko, Mary Shimoyama, Simon N. Twigger, Jiali Chen, Chin-Fu Chen, Chunyu Fan, Cindy Foote, Gopal R. Gopinath, Glenn Harris, Aubrey Hughes, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Natalya Nenasheva, Jeff Nie, Rajni Nigam, Victoria Petri, Dorothy Reilly, Weiye Wang, Wenhua Wu, Angela Zuniga-Meyer, Lan Zhao, Anne E. Kwitek, Peter J. Tonellato, Howard J. Jacob:
  The Rat Genome Database (RGD): developments towards a phenome database. 485-491
  
• Greta Petersen, Per Johnson, Lars Andersson, Karin Klinga-Levan, Pedro M. Gómez-Fabre, Fredrik Ståhl:
  RatMap - rat genome tools and data. 492-494
  
• Christian Roth, Matthew J. Betts, Pär Steffansson, Gisle Sælensminde, David A. Liberles:
  The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics. 495-497
  
• Tobias Penzkofer, Thomas Dandekar, Tomasz Zemojtel:
  L1Base: from functional annotation to prediction of active LINE-1 elements. 498-500
  
• Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott:
  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. 501-504
  
• Angelo Boccia, Mauro Petrillo, Diego di Bernardo, Alessandro Guffanti, Flavio Mignone, Stefano Confalonieri, Lucilla Luzi, Graziano Pesole, Giovanni Paolella, Andrea Ballabio, Sandro Banfi:
  DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. 505-510
  
• Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia:
  HCAD, closing the gap between breakpoints and genes. 511-513
  
• Ada Hamosh, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, Victor A. McKusick:
  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. 514-517
  
• Hyo Jin Kang, Kyoung Oak Choi, Byung-Dong Kim, Sangsoo Kim, Young Joo Kim:
  FESD: a Functional Element SNPs Database in human. 518-522
  
• James Robinson, Matthew J. Waller, Peter Stoehr, Steven G. E. Marsh:
  IPD - the Immuno Polymorphism Database. 523-526
  
• Joke Reumers, Joost Schymkowitz, Jesper Ferkinghoff-Borg, Francois Stricher, Luis Serrano, Frederic Rousseau:
  SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. 527-532
  
• Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai:
  Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. 533-536
  
• João Pedro de Magalhães, Joana Costa, Olivier Toussaint:
  HAGR: the Human Ageing Genomic Resources. 537-543
  
• Luc J. Smink, Erin M. Helton, Barry C. Healy, Christopher C. Cavnor, Alex C. Lam, Daisy Flamez, Oliver S. Burren, Yang Wang, Geoffrey E. Dolman, David B. Burdick, Vincent H. Everett, Gustavo Glusman, Davide Laneri, Lee Rowen, Helen Schuilenburg, Neil M. Walker, Josyf Mychaleckyj, Linda S. Wicker, Decio L. Eizirik, John A. Todd, Nathan Goodman:
  T1DBase, a community web-based resource for type 1 diabetes research. 544-549
  
• Yasuhiro Kasai, Shin-ichi Hashimoto, Tomoyuki Yamada, Jun Sese, Sumio Sugano, Kouji Matsushima, Shinichi Morishita:
  5'SAGE: 5'-end Serial Analysis of Gene Expression database. 550-552
  
• Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Niran Abeygunawardena, Sergio Contrino, Richard Coulson, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Misha Kapushesky, P. Lilja, Gaurab Mukherjee, Ahmet Oezcimen, Tim F. Rayner, Philippe Rocca-Serra, Anjan Sharma, Susanna-Assunta Sansone, Alvis Brazma:
  ArrayExpress - a public repository for microarray gene expression data at the EBI. 553-555
  
• Maxim Shklar, Liora Strichman-Almashanu, Orit Shmueli, Michael Shmoish, Marilyn Safran, Doron Lancet:
  GeneTide - Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases. 556-561
  
• Tanya Barrett, Tugba O. Suzek, Dennis B. Troup, Stephen E. Wilhite, Wing-Chi Ngau, Pierre Ledoux, Dmitry Rudnev, Alex E. Lash, Wataru Fujibuchi, Ron Edgar:
  NCBI GEO: mining millions of expression profiles - database and tools. 562-566
  
• Motohiko Tanino, Marie-Anne Debily, Takuro Tamura, Teruyoshi Hishiki, Osamu Ogasawara, Katsuji Murakawa, Shoko Kawamoto, Kouichi Itoh, Shinya Watanabe, Sandro José de Souza, Sandrine Imbeaud, Esther Graudens, Eric Eveno, Phillip Hilton, Yukio Sudo, Janet Kelso, Kazuho Ikeo, Tadashi Imanishi, Takashi Gojobori, Charles Auffray, Winston Hide, Kousaku Okubo:
  The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. 567-572
  
• Vishal Shah, Sriram Sridhar, Jennifer Beane, Jerome S. Brody, Avrum Spira:
  SIEGE: Smoking Induced Epithelial Gene Expression Database. 573-579
  
• Catherine A. Ball, Ihab A. B. Awad, Janos Demeter, Jeremy Gollub, Joan M. Hebert, Tina Hernandez-Boussard, Heng Jin, John C. Matese, Michael Nitzberg, Farrell Wymore, Zachariah K. Zachariah, Patrick O. Brown, Gavin Sherlock:
  The Stanford Microarray Database accommodates additional microarray platforms and data formats. 580-582
  
• Oliver Drews, Angelika Görg:
  DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels. 583-587
  
• Florencio Pazos, David Guijas, Alfonso Valencia, Victor de Lorenzo:
  MetaRouter: bioinformatics for bioremediation. 588-592
  
• Marie-Paule Lefranc, Véronique Giudicelli, Quentin Kaas, Elodie Duprat, Joumana Jabado-Michaloud, Dominique Scaviner, Chantal Ginestoux, Oliver Clément, Denys Chaume, Gérard Lefranc:
  IMGT, the international ImMunoGeneTics information system^®. 593-597
  
• Nuwee Wiwatwattana, Anuj Kumar:
  Organelle DB: a cross-species database of protein localization and function. 598-604
  
• Joshua L. Heazlewood, A. Harvey Millar:
  AMPDB: the Arabidopsis Mitochondrial Protein Database. 605-610
  
• Marty C. Brandon, Marie T. Lott, Kevin Cuong Nguyen, Syawal Spolim, Shamkant B. Navathe, Pierre Baldi, Douglas C. Wallace:
  MITOMAP: a human mitochondrial genome database - 2004 update. 611-613
  
• Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook, Roger P. Wise, Julie A. Dickerson:
  BarleyBase - an expression profiling database for plant genomics. 614-618
  
• C. Künne, Matthias Lange, T. Funke, H. Miehe, T. Thiel, Ivo Grosse, Uwe Scholz:
  CR-EST: a resource for crop ESTs. 619-621
  
• Stephen Rudd:
  openSputnik - a database to ESTablish comparative plant genomics using unsaturated sequence collections. 622-627
  
• Stephen Rudd, Heiko Schoof, Klaus F. X. Mayer:
  PlantMarkers - a database of predicted molecular markers from plants. 628-632
  
• John W. S. Brown, Peter J. Shaw, Paul Shaw, David F. Marshall:
  Arabidopsis nucleolar protein database (AtNoPDB). 633-636
  
• Adam M. Gustafson, Edwards Allen, Scott A. Givan, Daniel Smith, James C. Carrington, Kristin D. Kasschau:
  ASRP: the Arabidopsis Small RNA Project Database. 637-640
  
• Sébastien Aubourg, Véronique Brunaud, Clémence Bruyère, Mark Cock, Richard Cooke, Annick Cottet, Arnaud Couloux, Patrice Déhais, Gilbert Deléage, Aymeric Duclert, Manuel Echeverria, Aimée Eschbach, Denis Falconet, Ghislain Filippi, Christine Gaspin, Christophe Geourjon, Jean-Michel Grienenberger, Guy Houlné, Elisabeth Jamet, Frédéric Lechauve, Olivier Leleu, Philippe Leroy, Régis Mache, Christian Meyer, Hafed Nedjari, Ioan Negrutiu, Valérie Orsini, Eric Peyretaillade, Cyril Pommier, Jeroen Raes, Jean-Loup Risler, Stéphane Rivière, Stephane Rombauts, Pierre Rouzé, Michel Schneider, Philippe Schwob, Ian Small, Ghislain Soumayet-Kampetenga, Darko Stankovski, Claire Toffano, Michael Tognolli, Michel Caboche, Alain Lecharny:
  GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. 641-646
  
• Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Motoaki Seki, Takashi Kuromori, Takuya Ito, Akihiko Konagaya, Tetsuro Toyoda, Kazuo Shinozaki:
  RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. 647-650
  
• Yuichi Ito, Kohji Arikawa, Baltazar A. Antonio, Isamu Ohta, Shinji Naito, Yoshiyuki Mukai, Atsuko Shimano, Masatoshi Masukawa, Michie Shibata, Mayu Yamamoto, Yukiyo Ito, Junri Yokoyama, Yasumichi Sakai, Katsumi Sakata, Yoshiaki Nagamura, Nobukazu Namiki, Takashi Matsumoto, Kenichi Higo, Takuji Sasaki:
  Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics. 651-655
  
• Christopher G. Love, Andrew J. Robinson, Geraldine A. C. Lim, Clare J. Hopkins, Jacqueline Batley, Gary Barker, German C. Spangenberg, David Edwards:
  Brassica ASTRA: an integrated database for Brassica genomic research. 656-659
  
• Michael D. Gonzales, Eric Archuleta, Andrew D. Farmer, Kamal Gajendran, David Grant, Randy C. Shoemaker, William D. Beavis, Mark E. Waugh:
  The Legume Information System (LIS): an integrated information resource for comparative legume biology. 660-665
  
• Svenja Meyer, Axel Nagel, Christiane Gebhardt:
  PoMaMo - a comprehensive database for potato genome data. 666-670
  
• Ida Retter, Hans-Helmar Althaus, Richard Münch, Werner Müller:
  VBASE2, an integrative V gene database. 671-674
  
• Susie Stephens, Jake Yue Chen, Marcel G. Davidson, Shiby Thomas, Barry M. Trute:
  Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences. 675-679
  

Volume 33, Web-Server-Issue, July 1 2005

• Editorial. 1
  

• Joanne A. Fox, Stefanie L. Butland, Scott McMillan, Graeme Campbell, B. F. Francis Ouellette:
  The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers. 3-24
  
• Sharmila Pillai, Ville Silventoinen, Kimmo Kallio, M. Senger, Siamak Sobhany, John G. Tate, Samir S. Velankar, Adel Golovin, Kim Henrick, P. Rice, Peter Stoehr, Rodrigo Lopez:
  SOAP-based services provided by the European Bioinformatics Institute. 25-28
  
• Goran Neshich, Luiz C. Borro, Roberto H. Higa, Paula R. Kuser, Michel E. B. Yamagishi, Eduardo H. Franco, João N. Krauchenco, Renato Fileto, André A. Ribeiro, George B. P. Bezerra, Thiago M. Velludo, Tomás S. Jimenez, Noboru Furukawa, Hirofumi Teshima, Koji Kitajima, K. Abdulla Bava, Akinori Sarai, Roberto C. Togawa, Adauto L. Mancini:
  The Diamond STING server. 29-35
  
• Kevin Bryson, Liam J. McGuffin, Russell L. Marsden, Jonathan J. Ward, Jaspreet Singh Sodhi, David T. Jones:
  Protein structure prediction servers at University College London. 36-38
  
• Vladimir Sobolev, Eran Eyal, Sergey Gerzon, Vladimir Potapov, Mariana Babor, Jaime Prilusky, Marvin Edelman:
  SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. 39-43
  
• C. Alland, F. Moreews, D. Boens, M. Carpentier, S. Chiusa, Mathieu Lonquety, N. Renault, Y. Wong, H. Cantalloube, Jacques Chomilier, Joëlle Hochez, J. Pothier, Bruno O. Villoutreix, J. F. Zagury, Pierre Tufféry:
  RPBS: a web resource for structural bioinformatics. 44-49
  
• Alessandro Paiardini, Francesco Bossa, Stefano Pascarella:
  CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology. 50-55
  
• Gabriela G. Loots, Ivan Ovcharenko:
  Dcode.org anthology of comparative genomic tools. 56-64
  
• Jérôme Gracy, Laurent Chiche:
  PAT: a protein analysis toolkit for integrated biocomputing on the web. 65-71
  
• Jianlin Cheng, Arlo Z. Randall, Michael J. Sweredoski, Pierre Baldi:
  SCRATCH: a protein structure and structural feature prediction server. 72-76
  
• Ling-Hong Hung, Shing-Chung Ngan, Tianyun Liu, Ram Samudrala:
  PROTINFO: new algorithms for enhanced protein structure predictions. 77-80
  
• Ori Sasson, Michal Linial:
  ProTarget: automatic prediction of protein structure novelty. 81-84
  
• P. Ananthalakshmi, Ch. Kiran Kumar, M. Jeyasimhan, K. Sumathi, Krishna Sekar:
  Fragment Finder: a web-based software to identify similar three-dimensional structural motif. 85-88
  
• Roman A. Laskowski, James D. Watson, Janet M. Thornton:
  ProFunc: a server for predicting protein function from 3D structure. 89-93
  
• Guoli Wang, Roland L. Dunbrack Jr.:
  PISCES: recent improvements to a PDB sequence culling server. 94-98
  
• Vladimir A. Ivanisenko, Alexey M. Eroshkin, Nikolay A. Kolchanov:
  WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families. 99-104
  
• Dan Xie, Ao Li, Minghui Wang, Zhewen Fan, Huanqing Feng:
  LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST. 105-110
  
• Adam Zemla, Carol Ecale Zhou, Tom Slezak, Tom Kuczmarski, D. Rama, Clinton Torres, D. Sawicka, Daniel Barsky:
  AS2TS system for protein structure modeling and analysis. 111-115
  
• Emmanuel Quevillon, Ville Silventoinen, Sharmila Pillai, Nicola Harte, Nicola J. Mulder, Rolf Apweiler, Rodrigo Lopez:
  InterProScan: protein domains identifier. 116-120
  
• Maria Novatchkova, Michael Wildpaner, Dieter Schweizer, Frank Eisenhaber:
  PhyloDome - visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets. 121-125
  
• O. Krishnadev, N. Rekha, Shashi B. Pandit, S. Abhiman, S. Mohanty, L. S. Swapna, S. Gore, Narayanaswamy Srinivasan:
  PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families. 126-129
  
• Ganesan Pugalenthi, Govindaraju Archunan, Ramanathan Sowdhamini:
  DIAL: a web-based server for the automatic identification of structural domains in proteins. 130-132
  
• Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich:
  pdbFun: mass selection and fast comparison of annotated PDB residues. 133-137
  
• Pedro A. Reche, Ellis L. Reinherz:
  PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands. 138-142
  
• Manoj Bhasin, G. P. S. Raghava:
  GPCRsclass: a web tool for the classification of amine type of G-protein-coupled receptors. 143-147
  
• Yukimitsu Yabuki, Takahiko Muramatsu, Takatsugu Hirokawa, Hidehito Mukai, Makiko Suwa:
  GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model. 148-153
  
• Manish Kumar, Manoj Bhasin, Navjot K. Natt, G. P. S. Raghava:
  BhairPred: prediction of ß-hairpins in a protein from multiple alignment information using ANN and SVM techniques. 154-159
  
• Richard A. George, Kuang Lin, Jaap Heringa:
  Scooby-domain: prediction of globular domains in protein sequence. 160-163
  
• M. Michael Gromiha, Shandar Ahmad, Makiko Suwa:
  TMBETA-NET: discrimination and prediction of membrane spanning ß-strands in outer membrane proteins. 164-167
  
• Urmila Kulkarni-Kale, Shriram Bhosle, Ashok S. Kolaskar:
  CEP: a conformational epitope prediction server. 168-171
  
• Guanglan Zhang, Asif M. Khan, Kellathur N. Srinivasan, J. Thomas August, Vladimir Brusic:
  MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides. 172-179
  
• Guanglan Zhang, Kellathur N. Srinivasan, Anitha Veeramani, J. Thomas August, Vladimir Brusic:
  PRED^BALB/c: a system for the prediction of peptide binding to H2^d molecules, a haplotype of the BALB/c mouse. 180-183
  
• Yu Xue, Fengfeng Zhou, Minjie Zhu, Kashif Ahmed, Guoliang Chen, Xuebiao Yao:
  GPS: a comprehensive www server for phosphorylation sites prediction. 184-187
  
• Andrew G. Garrow, Alison Agnew, David R. Westhead:
  TMB-Hunt: a web server to screen sequence sets for transmembrane ß-barrel proteins. 188-192
  
• Hongyi Zhou, Chi Zhang, Song Liu, Yaoqi Zhou:
  Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations. 193-197
  
• Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, Rita Casadio:
  TRAMPLE: the transmembrane protein labelling environment. 198-201
  
• Manoj Bhasin, G. P. S. Raghava:
  Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences. 202-207
  
• Christina Backes, Jan Küntzer, Hans-Peter Lenhof, Nicole Comtesse, Eckart Meese:
  GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences. 208-213
  
• Andreas Bohne-Lang, Claus-Wilhelm von der Lieth:
  GlyProt: in silico glycosylation of proteins. 214-219
  
• Pankaj Kamra, Rajesh S. Gokhale, Debasisa Mohanty:
  SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites. 220-225
  
• Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Jorng-Tzong Horng:
  KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites. 226-229
  
• Fabrizio Ferrè, Peter Clote:
  DiANNA: a web server for disulfide connectivity prediction. 230-232
  
• Darby Tien-Hao Chang, Yen-Jen Oyang, Jung-Hsin Lin:
  MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. 233-238
  
• Markus Gruber, Johannes Söding, Andrei N. Lupas:
  REPPER - repeats and their periodicities in fibrous proteins. 239-243
  
• Johannes Söding, Andreas Biegert, Andrei N. Lupas:
  The HHpred interactive server for protein homology detection and structure prediction. 244-248
  
• Iddo Friedberg, Adam Godzik:
  Fragnostic: walking through protein structure space. 249-251
  
• Kristian Vlahovicek, Alessandro Pintar, Laavanya Parthasarathi, Oliviero Carugo, Sándor Pongor:
  CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures. 252-254
  
• Roee Gutman, Carine Berezin, Roy Wollman, Yossi Rosenberg, Nir Ben-Tal:
  QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns. 255-261
  
• Thomas Yan, Danny Yoo, Tanya Z. Berardini, Lukas A. Mueller, Dan C. Weems, Shuai Weng, J. Michael Cherry, Seung Yon Rhee:
  PatMatch: a program for finding patterns in peptide and nucleotide sequences. 262-266
  
• David La, Dennis R. Livesay:
  MINER: software for phylogenetic motif identification. 267-270
  
• Stefan Roepcke, Petko Fiziev, P. H. Seeburg, Martin Vingron:
  SVC: structured visualization of evolutionary sequence conservation. 271-273
  
• Saikat Chakrabarti, Prem A. Anand, Nitin Bhardwaj, Ganesan Pugalenthi, Ramanathan Sowdhamini:
  SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs. 274-276
  
• Iris Bahir, Michal Linial:
  ProTeus: identifying signatures in protein termini. 277-280
  
• Milana Frenkel-Morgenstern, Alice Singer, Hagit Bronfeld, Shmuel Pietrokovski:
  One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries. 281-283
  
• Lukasz Jaroszewski, Leszek Rychlewski, Zhanwen Li, Weizhong Li, Adam Godzik:
  FFAS03: a server for profile-profile sequence alignments. 284-288
  
• Victor A. Simossis, Jaap Heringa:
  PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. 289-294
  
• Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, Süleyman Cenk Sahinalp:
  Manipulating multiple sequence alignments via MaM and WebMaM. 295-298
  
• Meytal Landau, Itay Mayrose, Yossi Rosenberg, Fabian Glaser, Eric Martz, Tal Pupko, Nir Ben-Tal:
  ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. 299-302
  
• Csaba Magyar, M. Michael Gromiha, Gerard Pujadas, Gábor E. Tusnády, István Simon:
  SRide: a server for identifying stabilizing residues in proteins. 303-305
  
• Emidio Capriotti, Piero Fariselli, Rita Casadio:
  I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. 306-310
  
• Jessica Dantzer, Charles W. Moad, Randy Heiland, Sean D. Mooney:
  MutDB services: interactive structural analysis of mutation data. 311-314
  
• William C. Ray:
  MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features. 315-319
  
• Cédric Binisti, Ahmed Ali Salim, Pierre Tufféry:
  PPG: online generation of protein pictures and animations. 320-323
  
• Jason McDermott, Michal Guerquin, Zachary Frazier, Aaron N. Chang, Ram Samudrala:
  BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes. 324-325
  
• Didier Croes, Fabian Couche, Shoshana J. Wodak, Jacques van Helden:
  Metabolic PathFinding: inferring relevant pathways in biochemical networks. 326-330
  
• Utkan Ogmen, Ozlem Keskin, A. Selim Aytuna, Ruth Nussinov, Attila Gürsoy:
  PRISM: protein interactions by structural matching. 331-336
  
• Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson:
  SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. 337-341
  
• Jens Kleinjung, Franca Fraternali:
  POPSCOMP: an automated interaction analysis of biomolecular complexes. 342-346
  
• Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost, Alfonso Valencia:
  EVAcon: a protein contact prediction evaluation service. 347-351
  
• Zhenjun Hu, Joe Mellor, Jie Wu, Takuji Yamada, Dustin T. Holloway, Charles DeLisi:
  VisANT: data-integrating visual framework for biological networks and modules. 352-357
  
• Rajarshi Maiti, Gary H. Van Domselaar, David S. Wishart:
  MovieMaker: a web server for rapid rendering of protein motions and interactions. 358-362
  
• Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson:
  PatchDock and SymmDock: servers for rigid and symmetric docking. 363-367
  
• John C. Gordon, Jonathan B. Myers, Timothy Folta, Valia Shoja, Lenwood S. Heath, Alexey Onufriev:
  H++: a server for estimating pK_as and adding missing hydrogens to macromolecules. 368-371
  
• Maria A. Miteva, Pierre Tufféry, Bruno O. Villoutreix:
  PCE: web tools to compute protein continuum electrostatics. 372-375
  
• Brian D. Halligan, Victor Ruotti, Simon N. Twigger, Andrew S. Greene:
  DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy. 376-381
  
• Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano:
  The FoldX web server: an online force field. 382-388
  
• Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, Panayiotis V. Benos:
  enoLOGOS: a versatile web tool for energy normalized sequence logos. 389-392
  
• Stein Aerts, Peter Van Loo, Gert Thijs, Herbert Mayer, Rainer de Martin, Yves Moreau, Bart De Moor:
  TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. 393-396
  
• Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Lorenz Bülow, Reinhard Hehl:
  AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana. 397-402
  
• Ivan Ovcharenko, Marcelo A. Nobrega:
  Identifying synonymous regulatory elements in vertebrate genomes. 403-407
  
• Anil G. Jegga, Ashima Gupta, Sivakumar Gowrisankar, Mrunal A. Deshmukh, Steven Connolly, Kevin Finley, Bruce J. Aronow:
  CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes. 408-411
  
• Guandong Wang, Taotao Yu, Weixiong Zhang:
  WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar. 412-416
  
• Oleg V. Vishnevsky, Nikolay A. Kolchanov:
  ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters. 417-422
  
• Alessandro Di Cara, Karsten Schmidt, Brian A. Hemmings, Edward J. Oakeley:
  PromoterPlot: a graphical display of promoter similarities by pattern recognition. 423-426
  
• Matti Kankainen, Liisa Holm:
  POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets. 427-431
  
• D. S. Chekmenev, C. Haid, A. E. Kel:
  P-Match: transcription factor binding site search by combining patterns and weight matrices. 432-437
  
• Stefan Roepcke, Steffen Grossmann, Sven Rahmann, Martin Vingron:
  T-Reg Comparator: an analysis tool for the comparison of position weight matrices. 438-441
  
• David L. Corcoran, Eleanor Feingold, Panayiotis V. Benos:
  FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. 442-446
  
• Eugene Berezikov, Victor Guryev, Edwin Cuppen:
  CONREAL web server: identification and visualization of conserved transcription factor binding sites. 447-450
  
• John Besemer, Mark Borodovsky:
  GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. 451-454
  
• Gary H. Van Domselaar, Paul Stothard, Savita Shrivastava, Joseph A. Cruz, Anchi Guo, Xiaoli Dong, Paul Lu, Duane Szafron, Russell Greiner, David S. Wishart:
  BASys: a web server for automated bacterial genome annotation. 455-459
  
• Fátima Al-Shahrour, Pablo Minguez, Juan M. Vaquerizas, Lucía Conde, Joaquín Dopazo:
  BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. 460-464
  
• Mario Stanke, Burkhard Morgenstern:
  AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. 465-467
  
• Páll Ísólfur Ólason:
  Integrating protein annotation resources through the Distributed Annotation System. 468-470
  
• Stéphane Cruveiller, Jérôme Le Saux, David Vallenet, Aurélie Lajus, Stéphanie Bocs, Claudine Médigue:
  MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes. 471-479
  
• Lei Bao, Mi Zhou, Yan Cui:
  nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. 480-482
  
• Jinho Yoo, Bonghee Seo, Yangseok Kim:
  SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis. 483-488
  
• Ruifang Zhang, Zanhua Zhu, Hongming Zhu, Tu H. Nguyen, Fengxia Yao, Kun Xia, Desheng Liang, Chunyu Liu:
  SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design. 489-492
  
• David Savage, Jacqueline Batley, Timothy A. Erwin, Erica Logan, Christopher G. Love, Geraldine A. C. Lim, Emmanuel Mongin, Gary Barker, German C. Spangenberg, David Edwards:
  SNPServer: a real-time SNP discovery tool. 493-495
  
• Matthias Klaften, Martin Hrabé de Angelis:
  ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants. 496-500
  
• Lucía Conde, Juan M. Vaquerizas, Carles Ferrer-Costa, Xavier de la Cruz, Modesto Orozco, Joaquín Dopazo:
  PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. 501-505
  
• Eric W. Klee, Kyong Jin Shim, Michael A. Pickart, Stephen C. Ekker, Lynda B. M. Ellis:
  AMOD: a morpholino oligonucleotide selection tool. 506-511
  
• Bernard Fertil, Matthieu Massin, Sylvain Lespinats, Caroline Devic, Philippe Dumee, Alain Giron:
  GENSTYLE: exploration and analysis of DNA sequences with genomic signature. 512-515
  
• Jakob Fredslund, Leif Schauser, Lene H. Madsen, Niels Sandal, Jens Stougaard:
  PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs. 516-520
  
• Roman Rydzanicz, X. Sharon Zhao, Philip E. Johnson:
  Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production. 521-525
  
• Andreas Grote, Karsten Hiller, Maurice Scheer, Richard Münch, Bernd Nörtemann, Dietmar C. Hempel, Dieter Jahn:
  JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. 526-531
  
• Dirk Pöhler, Nadine Werner, Rasmus Steinkamp, Burkhard Morgenstern:
  Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC. 532-534
  
• Per Eystein Sæbø, Sten Morten Andersen, Jon Myrseth, Jon K. Laerdahl, Torbjørn Rognes:
  PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology. 535-539
  
• Laurent Noé, Gregory Kucherov:
  YASS: enhancing the sensitivity of DNA similarity search. 540-543
  
• John Rachlin, Chunming Ding, Charles Cantor, Simon Kasif:
  MuPlex: multi-objective multiplex PCR assay design. 544-547
  
• Steven Ringquist, Christopher Pecoraro, Crystal M. S. Gilchrist, Alexis Styche, William A. Rudert, Panayiotis V. Benos, Massimo Trucco:
  SOP³v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms. 548-552
  
• Chung-Yen Lin, Fan-Kai Lin, Chieh Hua Lin, Li-Wei Lai, Hsiu-Jun Hsu, Shu-Hwa Chen, Chao A. Hsiung:
  POWER: PhylOgenetic WEb Repeater - an integrated and user-optimized framework for biomolecular phylogenetic analysis. 553-556
  
• Stéphane Guindon, Franck Lethiec, Patrice Duroux, Olivier Gascuel:
  PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. 557-559
  
• Sacha A. F. T. van Hijum, Aldert L. Zomer, Oscar P. Kuipers, Jan Kok:
  Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. 560-566
  
• Rasmus Wernersson:
  FeatureExtract - extraction of sequence annotation made easy. 567-569
  
• Alejandro Panjkovich, Tomás Norambuena, Francisco Melo:
  dnaMATE: a consensus melting temperature prediction server for short DNA sequences. 570-572
  
• Eivind Tøstesen, Geir Ivar Jerstad, Eivind Hovig:
  Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles. 573-576
  
• Nicholas R. Markham, Michael Zuker:
  DINAMelt web server for nucleic acid melting prediction. 577-581
  
• Zeynep Arziman, Thomas Horn, Michael Boutros:
  E-RNAi: a web application to design optimized RNAi constructs. 582-588
  
• Yuki Naito, Tomoyuki Yamada, Takahiro Matsumiya, Kumiko Ui-Tei, Kaoru Saigo, Shinichi Morishita:
  dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. 589-591
  
• André Boorsma, Barrett C. Foat, Daniel J. Vis, Frans Klis, Harmen J. Bussemaker:
  T-profiler: scoring the activity of predefined groups of genes using gene expression data. 592-595
  
• Chang-Jiun Wu, Simon Kasif:
  GEMS: a web server for biclustering analysis of expression data. 596-599
  
• P. Clote:
  RNALOSS: a web server for RNA locally optimal secondary structures. 600-604
  
• A. Xayaphoummine, T. Bucher, H. Isambert:
  Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. 605-610
  
• Rasmus Wernersson, Henrik Bjørn Nielsen:
  OligoWiz 2.0 - integrating sequence feature annotation into the design of microarray probes. 611-615
  
• Juan M. Vaquerizas, Lucía Conde, Patricio Yankilevich, Amaya Cabezón, Pablo Minguez, Ramón Díaz-Uriarte, Fátima Al-Shahrour, Javier Herrero, Joaquín Dopazo:
  GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. 616-620
  
• Hee-Joon Chung, Chan Hee Park, Mi Ryung Han, Seokho Lee, Jung Hun Ohn, Jihoon Kim, Jihun Kim, Ju Han Kim:
  ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics. 621-626
  
• Albert Hsiao, Trey Ideker, Jerrold M. Olefsky, Shankar Subramaniam:
  VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. 627-632
  
• Bernhard Mlecnik, Marcel Scheideler, Hubert Hackl, Jürgen Hartler, Fatima Sanchez-Cabo, Zlatko Trajanoski:
  PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. 633-637
  
• Michael Psarros, Steffen Heber, Manuela Sick, Gnanasekaran Thoppae, Keith Harshman, Beate Sick:
  RACE: Remote Analysis Computation for gene Expression data. 638-643
  
• Chiara Romualdi, Nicola Vitulo, Micky Del Favero, Gerolamo Lanfranchi:
  MIDAW: a web tool for statistical analysis of microarray data. 644-649
  
• Jakob Hull Havgaard, Rune B. Lyngsø, Jan Gorodkin:
  The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. 650-653
  
• Shobhit Gupta, Martin Vingron, Stefan A. Haas:
  T-STAG: resource and web-interface for tissue-specific transcripts and genes. 654-658
  
• Sachiyo Aburatani, Kousuke Goto, Shigeru Saito, Hiroyuki Toh, Katsuhisa Horimoto:
  ASIAN: a web server for inferring a regulatory network framework from gene expression profiles. 659-664
  
• Giovanni Lavorgna, Riccardo Triunfo, Federico Santoni, Ugo Orfanelli, Sara Noci, Alessandro Bulfone, Gianluigi Zanetti, Giorgio Casari:
  AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts. 665-668
  
• Xiang Jia Min, Gregory Butler, Reginald Storms, Adrian Tsang:
  TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences. 669-672
  
• Xin Wu, Michael G. Walker, Jingchu Luo, Liping Wei:
  GBA server: EST-based digital gene expression profiling. 673-676
  
• Xiang Jia Min, Gregory Butler, Reginald Storms, Adrian Tsang:
  OrfPredictor: predicting protein-coding regions in EST-derived sequences. 677-680
  
• Namshin Kim, Dajeong Lim, Sanghyuk Lee, Heebal Kim:
  ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs. 681-685
  
• Peter Schattner, Angela N. Brooks, Todd M. Lowe:
  The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. 686-689
  
• Cei Abreu-Goodger, Enrique Merino:
  RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. 690-692
  
• Jean Pylouster, Catherine Sénamaud-Beaufort, Tula Ester Saison-Behmoaras:
  WEBSAGE: a web tool for visual analysis of differentially expressed human SAGE tags. 693-695
  
• Ventsislav Rusinov, Vesselin Baev, Ivan Nikiforov Minkov, Martin Tabler:
  MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence. 696-700
  
• Yuanji Zhang:
  miRU: an automated plant miRNA target prediction server. 701-704
  
• Andreas Bohne-Lang, Wolf-Dieter Groch, René Ranzinger:
  AISMIG - an interactive server-side molecule image generator. 705-709
  
• Alexander Goesmann, Burkhard Linke, Daniela Bartels, Michael Dondrup, Lutz Krause, Heiko Neuweger, Sebastian Oehm, Tobias Paczian, A. Wilke, Folker Meyer:
  BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. 710-716
  
• Marco Masseroli, Osvaldo Galati, Francesco Pinciroli:
  GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. 717-723
  
• Stephen Rudd, Igor V. Tetko:
  Éclair - a web service for unravelling species origin of sequences sampled from mixed host interfaces. 724-727
  
• David M. Aanensen, Brian G. Spratt:
  The multilocus sequence typing network: mlst.net. 728-733
  
• Tsute Chen, Kevin Abbey, Wen-jie Deng, Meng-chuan Cheng:
  The bioinformatics resource for oral pathogens. 734-740
  
• Bing Zhang, Stefan Kirov, Jay Snoddy:
  WebGestalt: an integrated system for exploring gene sets in various biological contexts. 741-748
  
• Peter Juvan, Janez Demsar, Gad Shaulsky, Blaz Zupan:
  GenePath: from mutations to genetic networks and back. 749-752
  
• Taro L. Saito, Jun Sese, Yoichiro Nakatani, Fumi Sano, Masashi Yukawa, Yoshikazu Ohya, Shinichi Morishita:
  Data mining tools for the Saccharomyces cerevisiae morphological database. 753-757
  
• M. A. van Driel, K. Cuelenaere, P. P. C. W. Kemmeren, Jack A. M. Leunissen, H. G. Brunner, Gert Vriend:
  GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. 758-761
  
• Purvesh Khatri, Sivakumar Sellamuthu, Pooja Malhotra, Kashyap Amin, Arina Done, Sorin Draghici:
  Recent additions and improvements to the Onto-Tools. 762-765
  
• M. L. Hekkelman, G. Vriend:
  MRS: a fast and compact retrieval system for biological data. 766-769
  
• Benjamin R. Landsteiner, Michael R. Olson, Robert Rutherford:
  Current Comparative Table (CCT) automates customized searches of dynamic biological databases. 770-773
  
• Thomas Götz, Claus-Wilhelm von der Lieth:
  PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts. 774-778
  
• Holger Maier, Stefanie Döhr, Korbinian Grote, Sean O'Keeffe, Thomas Werner, Martin Hrabé de Angelis, Ralf Schneider:
  LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts. 779-782
  
• Andreas Doms, Michael Schroeder:
  GoPubMed: exploring PubMed with the Gene Ontology. 783-786