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,