Nucleic Acids Research, Volume 33

Volume 33, Database-Issue, January 1 2005

• Alex Bateman:
  Editorial. 1
  Electronic Edition (link) BibTeX
• Dov Greenbaum, Andrew Smith, Mark Gerstein:
  Editorial. 3-4
  Electronic Edition (link) BibTeX

• Michael Y. Galperin:
  The Molecular Biology Database Collection: 2005 update. 5-24
  Electronic Edition (link) BibTeX
• Yoshio Tateno, Naruya Saitou, Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori:
  DDBJ in collaboration with mass-sequencing teams on annotation. 25-28
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
  GenBank. 34-38
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Catherine Brooksbank, Graham Cameron, Janet M. Thornton:
  The European Bioinformatics Institute's data resources: towards systems biology. 46-53
  Electronic Edition (link) BibTeX
• Donna R. Maglott, James Ostell, Kim D. Pruitt, Tatiana A. Tatusova:
  Entrez Gene: gene-centered information at NCBI. 54-58
  Electronic Edition (link) BibTeX
• Adel Khelifi, Laurent Duret, Dominique Mouchiroud:
  HOPPSIGEN: a database of human and mouse processed pseudogenes. 59-66
  Electronic Edition (link) BibTeX
• Victor G. Levitsky, Aleksey V. Katokhin, Olga A. Podkolodnaya, Dagmara P. Furman, Nikolay A. Kolchanov:
  NPRD: Nucleosome Positioning Region Database. 67-70
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Pora Kim, Namshin Kim, Younghee Lee, Bumjin Kim, Youngah Shin, Sanghyuk Lee:
  ECgene: genome annotation for alternative splicing. 75-79
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva:
  The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. 91-97
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Haibo Zhang, Jun Hu, Michael Recce, Bin Tian:
  PolyA_DB: a database for mammalian mRNA polyadenylation. 116-120
  Electronic Edition (link) BibTeX
• Sam Griffiths-Jones, Simon Moxon, Mhairi Marshall, Ajay Khanna, Sean R. Eddy, Alex Bateman:
  Rfam: annotating non-coding RNAs in complete genomes. 121-124
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Alistair M. Chalk, Richard E. Warfinge, Patrick Georgii-Hemming, Erik L. L. Sonnhammer:
  siRNAdb: a database of siRNA sequences. 131-134
  Electronic Edition (link) BibTeX
• James A. McCloskey, Jef Rozenski:
  The Small Subunit rRNA Modification Database. 135-138
  Electronic Edition (link) BibTeX
• Mathias Sprinzl, Konstantin S. Vassilenko:
  Compilation of tRNA sequences and sequences of tRNA genes. 139-140
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Amos Bairoch, Rolf Apweiler, Cathy H. Wu, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, María J. Martín, Darren A. Natale, Claire O'Donovan, Nicole Redaschi, Lai-Su L. Yeh:
  The Universal Protein Resource (UniProt). 154-159
  Electronic Edition (link) BibTeX
• Sven Mika, Burkhard Rost:
  NMPdb: Database of Nuclear Matrix Proteins. 160-163
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Qiaojuan Jane Su, Lin Lu, Serge Saxonov, Douglas L. Brutlag:
  eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity. 178-182
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Andreas Heger, Christopher Andrew Wilton, Ashwin Sivakumar, Liisa Holm:
  ADDA: a domain database with global coverage of the protein universe. 188-191
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Saraswathi Abhiman, Erik L. L. Sonnhammer:
  FunShift: a database of function shift analysis on protein subfamilies. 197-200
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• James A. Casbon, Mansoor A. S. Saqi:
  S4: structure-based sequence alignments of SCOP superfamilies. 219-222
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Thomas Meinel, Antje Krause, Hannes Luz, Martin Vingron, Eike Staub:
  The SYSTERS Protein Family Database in 2005. 226-229
  Electronic Edition (link) BibTeX
• Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
  REBASE - restriction enzymes and DNA methyltransferases. 230-232
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Thomas Lütteke, Martin Frank, Claus-Wilhelm von der Lieth:
  Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB. 242-246
  Electronic Edition (link) BibTeX
• 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 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
  Electronic Edition (link) BibTeX
• Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
  GenDiS: Genomic Distribution of protein structural domain Superfamilies. 252-255
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Samir S. Velankar, P. McNeil, V. Mittard-Runte, A. Suarez, Daniel Barrell, Rolf Apweiler, Kim Henrick:
  E-MSD: an integrated data resource for bioinformatics. 262-265
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Gábor E. Tusnády, Zsuzsanna Dosztányi, István Simon:
  PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. 275-278
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Jonathan D. Wren, Jeffrey T. Chang, James Pustejovsky, Eytan Adar, Harold R. Garner, Russ B. Altman:
  Biomedical term mapping databases. 289-293
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• José M. Peregrin-Alvarez, Andrew Yam, Gaya Sivakumar, John Parkinson:
  PartiGeneDB - collating partial genomes. 303-307
  Electronic Edition (link) BibTeX
• M. Louise Riley, Thorsten Schmidt, Christian Wagner, Hans-Werner Mewes, Dmitrij Frishman:
  The PEDANT genome database in 2005. 308-310
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Hiroyuki Ogata, Jean-Michel Claverie:
  Metagrowth: a new resource for the building of metabolic hypotheses in microbiology. 321-324
  Electronic Edition (link) BibTeX
• Lihong Chen, Jian Yang, Jun Yu, Zhijian Yao, Lilian Sun, Yan Shen, Qi Jin:
  VFDB: a reference database for bacterial virulence factors. 325-328
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Uma Maheswari, Anton Montsant, Johannes Goll, S. Krishnasamy, K. R. Rajyashri, Villoo Morawala Patell, Chris Bowler:
  The Diatom EST Database. 344-347
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Michael Riffle, Lars Malmström, Trisha N. Davis:
  The Yeast Resource Center Public Data Repository. 378-382
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Rachel A. Drysdale, Madeline A. Crosby:
  FlyBase: genes and gene models. 390-395
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Nozomi Nagano:
  EzCatDB: the Enzyme Catalytic-mechanism Database. 407-412
  Electronic Edition (link) BibTeX
• Amelie Stein, Robert B. Russell, Patrick Aloy:
  3did: interacting protein domains of known three-dimensional structure. 413-417
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Vamsi Veeramachaneni, Wojciech Makalowski:
  DED: Database of Evolutionary Distances. 442-446
  Electronic Edition (link) BibTeX
• 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, J. 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
  Electronic Edition (link) BibTeX
• Fan Hsu, Tom H. Pringle, Robert M. Kuhn, Donna Karolchik, Mark Diekhans, David Haussler, W. James Kent:
  The UCSC Proteome Browser. 454-458
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer:
  Inparanoid: a comprehensive database of eukaryotic orthologs. 476-480
  Electronic Edition (link) BibTeX
• Eric Bazin, Laurent Duret, Simon Penel, Nicolas Galtier:
  Polymorphix: a sequence polymorphism database. 481-484
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Greta Petersen, Per Johnson, Lars Andersson, Karin Klinga-Levan, Pedro M. Gómez-Fabre, Fredrik Ståhl:
  RatMap - rat genome tools and data. 492-494
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Tobias Penzkofer, Thomas Dandekar, Tomasz Zemojtel:
  L1Base: from functional annotation to prediction of active LINE-1 elements. 498-500
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Robert Hoffmann, Joaquín Dopazo, Juan C. Cigudosa, Alfonso Valencia:
  HCAD, closing the gap between breakpoints and genes. 511-513
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Hyo Jin Kang, Kyoung Oak Choi, Byung-Dong Kim, Sangsoo Kim, Young Joo Kim:
  FESD: a Functional Element SNPs Database in human. 518-522
  Electronic Edition (link) BibTeX
• James Robinson, Matthew J. Waller, Peter Stoehr, Steven G. E. Marsh:
  IPD - the Immuno Polymorphism Database. 523-526
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• João Pedro de Magalhães, Joana Costa, Olivier Toussaint:
  HAGR: the Human Ageing Genomic Resources. 537-543
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Niran Abeygunawardena, Sergio Contrino, R. Coulson, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, Misha Kapushesky, P. Lilja, Gaurab Mukherjee, Ahmet Oezcimen, Tim 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Vishal Shah, Sriram Sridhar, Jennifer Beane, Jerome S. Brody, Avrum Spira:
  SIEGE: Smoking Induced Epithelial Gene Expression Database. 573-579
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Oliver Drews, Angelika Görg:
  DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels. 583-587
  Electronic Edition (link) BibTeX
• Florencio Pazos, David Guijas, Alfonso Valencia, Victor de Lorenzo:
  MetaRouter: bioinformatics for bioremediation. 588-592
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Nuwee Wiwatwattana, Anuj Kumar:
  Organelle DB: a cross-species database of protein localization and function. 598-604
  Electronic Edition (link) BibTeX
• Joshua L. Heazlewood, A. Harvey Millar:
  AMPDB: the Arabidopsis Mitochondrial Protein Database. 605-610
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• C. Künne, Matthias Lange, T. Funke, H. Miehe, T. Thiel, Ivo Grosse, Uwe Scholz:
  CR-EST: a resource for crop ESTs. 619-621
  Electronic Edition (link) BibTeX
• Stephen Rudd:
  openSputnik - a database to ESTablish comparative plant genomics using unsaturated sequence collections. 622-627
  Electronic Edition (link) BibTeX
• Stephen Rudd, Heiko Schoof, Klaus F. X. Mayer:
  PlantMarkers - a database of predicted molecular markers from plants. 628-632
  Electronic Edition (link) BibTeX
• John W. S. Brown, Peter J. Shaw, Paul Shaw, David F. Marshall:
  Arabidopsis nucleolar protein database (AtNoPDB). 633-636
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Svenja Meyer, Axel Nagel, Christiane Gebhardt:
  PoMaMo - a comprehensive database for potato genome data. 666-670
  Electronic Edition (link) BibTeX
• Ida Retter, Hans Helmar Althaus, Richard Münch, Werner Müller:
  VBASE2, an integrative V gene database. 671-674
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX

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

• Editorial. 1
  Electronic Edition (link) BibTeX

• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Alessandro Paiardini, Francesco Bossa, Stefano Pascarella:
  CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology. 50-55
  Electronic Edition (link) BibTeX
• Gabriela G. Loots, Ivan Ovcharenko:
  Dcode.org anthology of comparative genomic tools. 56-64
  Electronic Edition (link) BibTeX
• Jérôme Gracy, Laurent Chiche:
  PAT: a protein analysis toolkit for integrated biocomputing on the web. 65-71
  Electronic Edition (link) BibTeX
• Jianlin Cheng, Arlo Z. Randall, Michael J. Sweredoski, Pierre Baldi:
  SCRATCH: a protein structure and structural feature prediction server. 72-76
  Electronic Edition (link) BibTeX
• Ling-Hong Hung, Shing-Chung Ngan, Tianyun Liu, Ram Samudrala:
  PROTINFO: new algorithms for enhanced protein structure predictions. 77-80
  Electronic Edition (link) BibTeX
• Ori Sasson, Michal Linial:
  ProTarget: automatic prediction of protein structure novelty. 81-84
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Roman A. Laskowski, James D. Watson, Janet M. Thornton:
  ProFunc: a server for predicting protein function from 3D structure. 89-93
  Electronic Edition (link) BibTeX
• Guoli Wang, Roland L. Dunbrack Jr.:
  PISCES: recent improvements to a PDB sequence culling server. 94-98
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Emmanuel Quevillon, Ville Silventoinen, Sharmila Pillai, Nicola Harte, Nicola J. Mulder, Rolf Apweiler, Rodrigo Lopez:
  InterProScan: protein domains identifier. 116-120
  Electronic Edition (link) BibTeX
• Maria Novatchkova, Michael Wildpaner, Dieter Schweizer, Frank Eisenhaber:
  PhyloDome - visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets. 121-125
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Ganesan Pugalenthi, Govindaraju Archunan, Ramanathan Sowdhamini:
  DIAL: a web-based server for the automatic identification of structural domains in proteins. 130-132
  Electronic Edition (link) BibTeX
• Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich:
  pdbFun: mass selection and fast comparison of annotated PDB residues. 133-137
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Manoj Bhasin, G. P. S. Raghava:
  GPCRsclass: a web tool for the classification of amine type of G-protein-coupled receptors. 143-147
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Richard A. George, Kuang Lin, Jaap Heringa:
  Scooby-domain: prediction of globular domains in protein sequence. 160-163
  Electronic Edition (link) BibTeX
• M. Michael Gromiha, Shandar Ahmad, Makiko Suwa:
  TMBETA-NET: discrimination and prediction of membrane spanning ß-strands in outer membrane proteins. 164-167
  Electronic Edition (link) BibTeX
• Urmila Kulkarni-Kale, Shriram Bhosle, Ashok S. Kolaskar:
  CEP: a conformational epitope prediction server. 168-171
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Yu Xue, Fengfeng Zhou, Minjie Zhu, Kashif Ahmed, Guoliang Chen, Xuebiao Yao:
  GPS: a comprehensive www server for phosphorylation sites prediction. 184-187
  Electronic Edition (link) BibTeX
• Andrew G. Garrow, Alison Agnew, David R. Westhead:
  TMB-Hunt: a web server to screen sequence sets for transmembrane ß-barrel proteins. 188-192
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, Rita Casadio:
  TRAMPLE: the transmembrane protein labelling environment. 198-201
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Andreas Bohne-Lang, Claus-Wilhelm von der Lieth:
  GlyProt: in silico glycosylation of proteins. 214-219
  Electronic Edition (link) BibTeX
• Pankaj Kamra, Rajesh S. Gokhale, Debasisa Mohanty:
  SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites. 220-225
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Fabrizio Ferrè, Peter Clote:
  DiANNA: a web server for disulfide connectivity prediction. 230-232
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Markus Gruber, Johannes Söding, Andrei N. Lupas:
  REPPER - repeats and their periodicities in fibrous proteins. 239-243
  Electronic Edition (link) BibTeX
• Johannes Söding, Andreas Biegert, Andrei N. Lupas:
  The HHpred interactive server for protein homology detection and structure prediction. 244-248
  Electronic Edition (link) BibTeX
• Iddo Friedberg, Adam Godzik:
  Fragnostic: walking through protein structure space. 249-251
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Roee Gutman, Carine Berezin, Roy Wollman, Yossi Rosenberg, Nir Ben-Tal:
  QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns. 255-261
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• David La, Dennis R. Livesay:
  MINER: software for phylogenetic motif identification. 267-270
  Electronic Edition (link) BibTeX
• Stefan Roepcke, Petko Fiziev, P. H. Seeburg, Martin Vingron:
  SVC: structured visualization of evolutionary sequence conservation. 271-273
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Iris Bahir, Michal Linial:
  ProTeus: identifying signatures in protein termini. 277-280
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Lukasz Jaroszewski, Leszek Rychlewski, Zhanwen Li, Weizhong Li, Adam Godzik:
  FFAS03: a server for profile-profile sequence alignments. 284-288
  Electronic Edition (link) BibTeX
• Victor A. Simossis, Jaap Heringa:
  PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. 289-294
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Csaba Magyar, M. Michael Gromiha, Gerard Pujadas, Gábor E. Tusnády, István Simon:
  SRide: a server for identifying stabilizing residues in proteins. 303-305
  Electronic Edition (link) BibTeX
• Emidio Capriotti, Piero Fariselli, Rita Casadio:
  I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. 306-310
  Electronic Edition (link) BibTeX
• Jessica Dantzer, Charles W. Moad, Randy Heiland, Sean D. Mooney:
  MutDB services: interactive structural analysis of mutation data. 311-314
  Electronic Edition (link) BibTeX
• William C. Ray:
  MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features. 315-319
  Electronic Edition (link) BibTeX
• Cédric Binisti, Ahmed Ali Salim, Pierre Tufféry:
  PPG: online generation of protein pictures and animations. 320-323
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Didier Croes, Fabian Couche, Shoshana J. Wodak, Jacques van Helden:
  Metabolic PathFinding: inferring relevant pathways in biochemical networks. 326-330
  Electronic Edition (link) BibTeX
• Utkan Ogmen, Ozlem Keskin, A. Selim Aytuna, Ruth Nussinov, Attila Gürsoy:
  PRISM: protein interactions by structural matching. 331-336
  Electronic Edition (link) BibTeX
• Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson:
  SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. 337-341
  Electronic Edition (link) BibTeX
• Jens Kleinjung, Franca Fraternali:
  POPSCOMP: an automated interaction analysis of biomolecular complexes. 342-346
  Electronic Edition (link) BibTeX
• Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost, Alfonso Valencia:
  EVAcon: a protein contact prediction evaluation service. 347-351
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Rajarshi Maiti, Gary H. Van Domselaar, David S. Wishart:
  MovieMaker: a web server for rapid rendering of protein motions and interactions. 358-362
  Electronic Edition (link) BibTeX
• Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson:
  PatchDock and SymmDock: servers for rigid and symmetric docking. 363-367
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Maria A. Miteva, Pierre Tufféry, Bruno O. Villoutreix:
  PCE: web tools to compute protein continuum electrostatics. 372-375
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, Luis Serrano:
  The FoldX web server: an online force field. 382-388
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Ivan Ovcharenko, Marcelo A. Nobrega:
  Identifying synonymous regulatory elements in vertebrate genomes. 403-407
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Guandong Wang, Taotao Yu, Weixiong Zhang:
  WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar. 412-416
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Alessandro Di Cara, Karsten Schmidt, Brian A. Hemmings, Edward J. Oakeley:
  PromoterPlot: a graphical display of promoter similarities by pattern recognition. 423-426
  Electronic Edition (link) BibTeX
• Matti Kankainen, Liisa Holm:
  POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets. 427-431
  Electronic Edition (link) BibTeX
• D. S. Chekmenev, C. Haid, A. E. Kel:
  P-Match: transcription factor binding site search by combining patterns and weight matrices. 432-437
  Electronic Edition (link) BibTeX
• Stefan Roepcke, Steffen Grossmann, Sven Rahmann, Martin Vingron:
  T-Reg Comparator: an analysis tool for the comparison of position weight matrices. 438-441
  Electronic Edition (link) BibTeX
• David L. Corcoran, Eleanor Feingold, Panayiotis V. Benos:
  FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. 442-446
  Electronic Edition (link) BibTeX
• Eugene Berezikov, Victor Guryev, Edwin Cuppen:
  CONREAL web server: identification and visualization of conserved transcription factor binding sites. 447-450
  Electronic Edition (link) BibTeX
• John Besemer, Mark Borodovsky:
  GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. 451-454
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Mario Stanke, Burkhard Morgenstern:
  AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. 465-467
  Electronic Edition (link) BibTeX
• Páll Ísólfur Ólason:
  Integrating protein annotation resources through the Distributed Annotation System. 468-470
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Lei Bao, Mi Zhou, Yan Cui:
  nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. 480-482
  Electronic Edition (link) BibTeX
• Jinho Yoo, Bonghee Seo, Yangseok Kim:
  SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis. 483-488
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Eric W. Klee, Kyong Jin Shim, Michael A. Pickart, Stephen C. Ekker, Lynda B. M. Ellis:
  AMOD: a morpholino oligonucleotide selection tool. 506-511
  Electronic Edition (link) BibTeX
• Bernard Fertil, Matthieu Massin, Sylvain Lespinats, Caroline Devic, Philippe Dumee, Alain Giron:
  GENSTYLE: exploration and analysis of DNA sequences with genomic signature. 512-515
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Dirk Pöhler, Nadine Werner, Rasmus Steinkamp, Burkhard Morgenstern:
  Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC. 532-534
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Laurent Noé, Gregory Kucherov:
  YASS: enhancing the sensitivity of DNA similarity search. 540-543
  Electronic Edition (link) BibTeX
• John Rachlin, Chunming Ding, Charles Cantor, Simon Kasif:
  MuPlex: multi-objective multiplex PCR assay design. 544-547
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Stéphane Guindon, Franck Lethiec, Patrice Duroux, Olivier Gascuel:
  PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. 557-559
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Rasmus Wernersson:
  FeatureExtract - extraction of sequence annotation made easy. 567-569
  Electronic Edition (link) BibTeX
• Alejandro Panjkovich, Tomás Norambuena, Francisco Melo:
  dnaMATE: a consensus melting temperature prediction server for short DNA sequences. 570-572
  Electronic Edition (link) BibTeX
• Eivind Tøstesen, Geir Ivar Jerstad, Eivind Hovig:
  Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles. 573-576
  Electronic Edition (link) BibTeX
• Nicholas R. Markham, Michael Zuker:
  DINAMelt web server for nucleic acid melting prediction. 577-581
  Electronic Edition (link) BibTeX
• Zeynep Arziman, Thomas Horn, Michael Boutros:
  E-RNAi: a web application to design optimized RNAi constructs. 582-588
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• André Boorsma, Barrett C. Foat, Daniel Vis, Frans Klis, Harmen J. Bussemaker:
  T-profiler: scoring the activity of predefined groups of genes using gene expression data. 592-595
  Electronic Edition (link) BibTeX
• Chang-Jiun Wu, Simon Kasif:
  GEMS: a web server for biclustering analysis of expression data. 596-599
  Electronic Edition (link) BibTeX
• P. Clote:
  RNALOSS: a web server for RNA locally optimal secondary structures. 600-604
  Electronic Edition (link) BibTeX
• A. Xayaphoummine, T. Bucher, H. Isambert:
  Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. 605-610
  Electronic Edition (link) BibTeX
• Rasmus Wernersson, Henrik Bjørn Nielsen:
  OligoWiz 2.0 - integrating sequence feature annotation into the design of microarray probes. 611-615
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Michael Psarros, Steffen Heber, Manuela Sick, Gnanasekaran Thoppae, Keith Harshman, Beate Sick:
  RACE: Remote Analysis Computation for gene Expression data. 638-643
  Electronic Edition (link) BibTeX
• Chiara Romualdi, Nicola Vitulo, Micky Del Favero, Gerolamo Lanfranchi:
  MIDAW: a web tool for statistical analysis of microarray data. 644-649
  Electronic Edition (link) BibTeX
• Jakob Hull Havgaard, Rune B. Lyngsø, Jan Gorodkin:
  The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. 650-653
  Electronic Edition (link) BibTeX
• Shobhit Gupta, Martin Vingron, Stefan A. Haas:
  T-STAG: resource and web-interface for tissue-specific transcripts and genes. 654-658
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Xiang Jia Min, Gregory Butler, Reginald Storms, Adrian Tsang:
  TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences. 669-672
  Electronic Edition (link) BibTeX
• Xin Wu, Michael G. Walker, Jingchu Luo, Liping Wei:
  GBA server: EST-based digital gene expression profiling. 673-676
  Electronic Edition (link) BibTeX
• Xiang Jia Min, Gregory Butler, Reginald Storms, Adrian Tsang:
  OrfPredictor: predicting protein-coding regions in EST-derived sequences. 677-680
  Electronic Edition (link) BibTeX
• Namshin Kim, Dajeong Lim, Sanghyuk Lee, Heebal Kim:
  ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs. 681-685
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Cei Abreu-Goodger, Enrique Merino:
  RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements. 690-692
  Electronic Edition (link) BibTeX
• Jean Pylouster, Catherine Sénamaud-Beaufort, Tula Ester Saison-Behmoaras:
  WEBSAGE: a web tool for visual analysis of differentially expressed human SAGE tags. 693-695
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Yuanji Zhang:
  miRU: an automated plant miRNA target prediction server. 701-704
  Electronic Edition (link) BibTeX
• Andreas Bohne-Lang, Wolf-Dieter Groch, René Ranzinger:
  AISMIG - an interactive server-side molecule image generator. 705-709
  Electronic Edition (link) BibTeX
• A. Goesmann, B. Linke, D. Bartels, M. Dondrup, L. Krause, H. Neuweger, S. Oehm, T. Paczian, A. Wilke, F. Meyer:
  BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. 710-716
  Electronic Edition (link) BibTeX
• Marco Masseroli, Osvaldo Galati, Francesco Pinciroli:
  GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. 717-723
  Electronic Edition (link) BibTeX
• Stephen Rudd, Igor V. Tetko:
  Éclair - a web service for unravelling species origin of sequences sampled from mixed host interfaces. 724-727
  Electronic Edition (link) BibTeX
• David M. Aanensen, Brian G. Spratt:
  The multilocus sequence typing network: mlst.net. 728-733
  Electronic Edition (link) BibTeX
• Tsute Chen, Kevin Abbey, Wen-jie Deng, Meng-chuan Cheng:
  The bioinformatics resource for oral pathogens. 734-740
  Electronic Edition (link) BibTeX
• Bing Zhang, Stefan Kirov, Jay Snoddy:
  WebGestalt: an integrated system for exploring gene sets in various biological contexts. 741-748
  Electronic Edition (link) BibTeX
• Peter Juvan, Janez Demsar, Gad Shaulsky, Blaz Zupan:
  GenePath: from mutations to genetic networks and back. 749-752
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• M. A. van Driel, K. Cuelenaere, P. P. C. W. Kemmeren, J. A. M. Leunissen, H. G. Brunner, Gert Vriend:
  GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. 758-761
  Electronic Edition (link) BibTeX
• Purvesh Khatri, Sivakumar Sellamuthu, Pooja Malhotra, Kashyap Amin, Arina Done, Sorin Draghici:
  Recent additions and improvements to the Onto-Tools. 762-765
  Electronic Edition (link) BibTeX
• M. L. Hekkelman, G. Vriend:
  MRS: a fast and compact retrieval system for biological data. 766-769
  Electronic Edition (link) BibTeX
• Benjamin R. Landsteiner, Michael R. Olson, Robert Rutherford:
  Current Comparative Table (CCT) automates customized searches of dynamic biological databases. 770-773
  Electronic Edition (link) BibTeX
• Thomas Götz, Claus-Wilhelm von der Lieth:
  PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts. 774-778
  Electronic Edition (link) BibTeX
• 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
  Electronic Edition (link) BibTeX
• Andreas Doms, Michael Schroeder:
  GoPubMed: exploring PubMed with the Gene Ontology. 783-786
  Electronic Edition (link) BibTeX