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ORCIDNucleic Acids Research, Volume 32
Volume 32, Database-Issue, January 1 2004
- Michael Y. Galperin
:
The Molecular Biology Database Collection: 2004 update. 3-22 - Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
GenBank: update. 23-26 - Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Y. Eberhardt, Nadeem Faruque, Maria Garcia-Pastor, Nicola Harte, Carola Kanz, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Peter Stoehr, Guenter Stoesser, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler:
The EMBL Nucleotide Sequence Database. 27-30 - Satoru Miyazaki, Hideaki Sugawara, Kazuho Ikeo, Takashi Gojobori, Yoshio Tateno:
DBJ in the stream of various biological data. 31-34 - David L. Wheeler, Deanna M. Church, Ron Edgar, Scott Federhen, Wolfgang Helmberg, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tugba O. Suzek, Tatiana A. Tatusova, Lukas Wagner:
atabase resources of the National Center for Biotechnology Information: update. 35-40 - Hans-Werner Mewes, Clara Amid, Roland Arnold, Dmitrij Frishman, Ulrich Güldener, Gertrud Mannhaupt, Martin Münsterkötter, Philipp Pagel, Normann Strack, Volker Stümpflen, Jens Warfsmann, Andreas Ruepp:
MIPS: analysis and annotation of proteins from whole genomes. 41-44 - Raphaël Leplae, Aline Hebrant, Shoshana J. Wodak, Ariane Toussaint:
ACLAME: A CLAssification of Mobile genetic Elements. 45-49 - Jan Paces, Adam Pavlícek, Radek Zika, Vladimir V. Kapitonov, Jerzy Jurka, Václav Paces:
HERVd: the Human Endogenous RetroViruses Database: update. 50 - Thierry-Pascal Baum, Nicolas Pasqual, Florence Thuderoz, Vivien Hierle, Denys Chaume, Marie-Paule Lefranc, Evelyne Jouvin-Marche, Patrice-Noël Marche, Jacques Demongeot:
IMGT/GeneInfo: enhancing V(D)J recombination database accessibility. 51-54 - Yogita Mantri, Kelly P. Williams:
Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities. 55-58 - Vivek Gopalan, Tin Wee Tan, Bernett T. K. Lee, Shoba Ranganathan:
Xpro: database of eukaryotic protein-encoding genes. 59-63 - Thangavel Alphonse Thanaraj, Stefan Stamm, Francis Clark, Jean-Jack M. Riethoven, Vincent Le Texier, Juha Muilu:
ASD: the Alternative Splicing Database. 64-69 - Heike Pospisil, Alexander Herrmann, Ralf H. Bortfeldt, Jens G. Reich:
EASED: Extended Alternatively Spliced EST Database. 70-74 - Yuko Makita, Mitsuteru Nakao, Naotake Ogasawara, Kenta Nakai:
BTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. 75-77 - Yutaka Suzuki, Riu Yamashita, Sumio Sugano, Kenta Nakai:
BTSS, DataBase of Transcriptional Start Sites: progress report 2004. 78-81 - Christoph D. Schmid, Viviane Praz, Mauro Delorenzi, Rouaïda Périer, Philipp Bucher:
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. 82-85 - Twyla T. Pohar, Hao Sun, Ramana V. Davuluri:
HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. 86-90 - Albin Sandelin, Wynand Alkema, Pär G. Engström, Wyeth W. Wasserman, Boris Lenhard:
JASPAR: an open-access database for eukaryotic transcription factor binding profiles. 91-94 - Jennifer F. Lee, Jay R. Hesselberth, Lauren Ancel Meyers, Andrew D. Ellington:
Aptamer Database. 95-100 - Jan Wuyts, Guy Perrière, Yves Van de Peer:
The European ribosomal RNA database. 101-103 - Pulcherie Gueneau de Novoa, Kelly P. Williams:
The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts. 104-108 - Sam Griffiths-Jones:
The microRNA Registry. 109-111 - Cathy H. Wu, Anastasia N. Nikolskaya, Hongzhan Huang, Lai-Su L. Yeh, Darren A. Natale, Cholanayakanahalli R. Vinayaka, Zhang-Zhi Hu, Raja Mazumder, Sandeep Kumar, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Leslie Arminski, Yongxing Chen, Jian Zhang, Jorge Louie Cardenas, Sehee Chung, Jorge Castro-Alvear, Georgi Dinkov, Winona C. Barker:
PIRSF: family classification system at the Protein Information Resource. 112-114 - Rolf Apweiler, Amos Bairoch, 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:
UniProt: the Universal Protein knowledgebase. 115-119 - K. Abdulla Bava, M. Michael Gromiha, Hatsuho Uedaira, Koji Kitajima, Akinori Sarai:
ProTherm, version 4.0: thermodynamic database for proteins and mutants. 120-121 - Tao Guo, Sujun Hua, Xinglai Ji, Zhirong Sun:
BSubLoc: database of protein subcellular localization. 122-124 - S. A. Fernando, P. Selvarani, Soma Das, Ch. Kiran Kumar, Sukanta Mondal, S. Ramakumar, Krishna Sekar:
THGS: a web-based database of Transmembrane Helices in Genome Sequences. 125-128 - Craig T. Porter, Gail J. Bartlett, Janet M. Thornton:
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. 129-133 - Nicolas Hulo, Christian J. A. Sigrist, Virginie Le Saux, Petra S. Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, Amos Bairoch:
Recent improvements to the PROSITE database. 134-137 - Alex Bateman, Lachlan James M. Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Sam Griffiths-Jones, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, Sean R. Eddy:
The Pfam protein families database. 138-141 - Ivica Letunic, Richard R. Copley, Steffen Schmidt, Francesca D. Ciccarelli, Tobias Doerks, Jörg Schultz, Chris P. Ponting, Peer Bork:
SMART 4.0: towards genomic data integration. 142-144 - Thierry Hotelier, Ludovic Renault, Xavier Cousin, Vincent Nègre, Pascale Marchot, Arnaud Chatonnet:
ESTHER, the database of the /?hydrolase fold superfamily of proteins. 145-147 - David A. Lee, Sandrine Fefeu, Adrian A. Edo-Ukeh, Christine A. Orengo, Christine Slingsby:
EyeSite: a semi-automated database of protein families in the eye. 148-152 - A. Krupa, K. R. Abhinandan, Narayanaswamy Srinivasan:
KinG: a database of protein kinases in genomes. 153-155 - Jean-Christophe Gelly, Jérôme Gracy, Quentin Kaas, Dung Le-Nguyen, Annie Heitz, Laurent Chiche:
The KNOTTIN website and database: a new information system dedicated to the knottin scaffold. 156-159 - Neil D. Rawlings, Dominic P. Tolle, Alan J. Barrett:
MEROPS: the peptidase database. 160-164 - David Ruau, Jorge Duarte, Tarik Ourjdal, Guy Perrière, Vincent Laudet, Marc Robinson-Rechavi:
Update of NUREBASE: nuclear hormone receptor functional genomics. 165-167 - Akihiro Nakao, Maki Yoshihama, Naoya Kenmochi:
RPG: the Ribosomal Protein Gene database. 168-170 - Antonio Hermoso, Daniel Aguilar, Francesc X. Avilés, Enrique Querol:
TrSDB: a proteome database of transcription factors. 171-173 - Michael M. Hoffman, Maksim A. Khrapov, J. Colin Cox, Jianchao Yao, Lingnan Tong, Andrew D. Ellington:
AANT: the Amino Aciduchleotide Interaction Database. 174-181 - Makio Tamura, Donna K. Hendrix, Peter S. Klosterman, Nancy R. B. Schimmelman, Steven E. Brenner, Stephen R. Holbrook:
SCOR: Structural Classification of RNA, version 2.0. 182-184 - Jordi Espadaler, Narcis Fernandez-Fuentes, Antonio Hermoso, Enrique Querol, Francesc X. Avilés, Michael J. E. Sternberg, Baldomero Oliva:
ArchDB: automated protein loop classification as a tool for structural genomics. 185-188 - John-Marc Chandonia, Gary Chung Hon, Nigel S. Walker, Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner:
The ASTRAL Compendium in 2004. 189-192 - R. Aroul Selvam, Rajkumar Sasidharan:
omIns: a web resource for domain insertions in known protein structures. 193-195 - Liam J. McGuffin, Stefano A. Street, Kevin Bryson, Søren-Aksel Sørensen, David T. Jones:
The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. 196-199 - A. Vinayagam, Ganesan Pugalenthi, R. Rajesh, Ramanathan Sowdhamini:
SDBASE: a consortium of native and modelled disulphide bonds in proteins. 200-202 - Lucy A. Stebbings, Kenji Mizuguchi:
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. 203-207 - Quentin Kaas, Manuel Ruiz, Marie-Paule Lefranc:
IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. 208-210 - Adel Golovin, Thomas J. Oldfield, John G. Tate, Samir S. Velankar, Geoffrey J. Barton, Harry Boutselakis, Dimitris Dimitropoulos, Joël Fillon, A. Hussain, John M. C. Ionides, Melford John, Peter A. Keller, Evgeny B. Krissinel, P. McNeil, Avi Naim, Richard H. Newman, Anne Pajon, Jorge Pineda, Abdel-Krim Rachedi, J. Copeland, Andrey Sitnov, Siamak Sobhany, Antonio Suarez-Uruena, G. J. Swaminathan, Mohammed Tagari, Swen Tromm, Wim F. Vranken, Kim Henrick:
E-MSD: an integrated data resource for bioinformatics. 211-216 - Ursula Pieper, Narayanan Eswar, Hannes Braberg, Mallur S. Madhusudhan, Fred P. Davis, Ashley C. Stuart, Nebojsa Mirkovic, Andrea Rossi, Marc A. Martí-Renom, András Fiser, Ben M. Webb, Daniel M. Greenblatt, Conrad C. Huang, Thomas E. Ferrin, Andrej Sali:
MODBASE, a database of annotated comparative protein structure models, and associated resources. 217-222 - Philip E. Bourne, Kenneth J. Addess, Wolfgang Bluhm, Li Chen, Nita Deshpande, Zukang Feng, Ward Fleri, Rachel Kramer Green, Jeffrey C. Merino-Ott, Wayne Townsend-Merino, Helge Weissig, John D. Westbrook, Helen M. Berman:
The distribution and query systems of the RCSB Protein Data Bank. 223-225 - Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin:
SCOP database in 2004: refinements integrate structure and sequence family data. 226-229 - Jürgen Kopp, Torsten Schwede:
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. 230-234 - Martin Madera, Christine Vogel, Sarah K. Kummerfeld, Cyrus Chothia, Julian Gough:
The SUPERFAMILY database in 2004: additions and improvements. 235-239 - Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich:
SURFACE: a database of protein surface regions for functional annotation. 240-244 - Keiran Fleming, Arne Müller, Robert M. MacCallum, Michael J. E. Sternberg:
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. 245-250 - Ioannis Michalopoulos, Gilleain M. Torrance, David R. Gilbert, David R. Westhead:
TOPS: an enhanced database of protein structural topology. 251-254 - Hester M. Wain, Michael J. Lush, Fabrice Ducluzeau, Varsha K. Khodiyar, Sue Povey:
Genew: the Human Gene Nomenclature Database, 2004 updates. 255-257 - Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource. 258-261
- Evelyn Camon, Michele Magrane, Daniel Barrell, Vivian Lee, Emily Dimmer, John Maslen, David Binns, Nicola Harte, Rodrigo Lopez, Rolf Apweiler:
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. 262-266 - Olivier Bodenreider:
The Unified Medical Language System (UMLS): integrating biomedical terminology. 267-270 - Ren Zhang, Hong-Yu Ou, Chun-Ting Zhang:
EG: a database of essential genes. 271-272 - Karsten Suhre, Jean-Michel Claverie:
FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. 273-276 - Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Yasushi Okuno, Masahiro Hattori:
The KEGG resource for deciphering the genome. 277-280 - Naomi Siew, Yaniv Azaria, Daniel Fischer:
The ORFanage: an ORFan database. 281-283 - Qinghu Ren, Katherine H. Kang, Ian T. Paulsen:
TransportDB: a relational database of cellular membrane transport systems. 284-288 - Urmila Kulkarni-Kale, Shriram Bhosle, G. Sunitha Manjari, Ashok S. Kolaskar:
VirGen: a comprehensive viral genome resource. 289-292 - Shan Sundararaj, Anchi Guo, Bahram Habibi-Nazhad, Melania Rouani, Paul Stothard, Michael Ellison, David S. Wishart:
The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. 293-295 - Roy R. Chaudhuri, Arshad M. Khan, Mark J. Pallen:
coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. 296-299 - Margrethe H. Serres, Sulip Goswami, Monica Riley:
GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. 300-302 - Heladia Salgado, Socorro Gama-Castro, Agustino Martínez-Antonio, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Martín Peralta-Gil, Delfino Garcia-Alonso, Verónica Jiménez-Jacinto, Alberto Santos-Zavaleta, César Bonavides-Martínez, Julio Collado-Vides:
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. 303-306 - Aurélien Barré, Antoine de Daruvar, Alain Blanchard:
MolliGen, a database dedicated to the comparative genomics of Mollicutes. 307-310 - Karen R. Christie, Shuai Weng, Rama Balakrishnan, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert S. Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, J. Michael Cherry:
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. 311-314 - David James Sherman, Pascal Durrens, Emmanuelle Beyne, Macha Nikolski:
Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. 315-318 - Taro L. Saito, Miwaka Ohtani, Hiroshi Sawai, Fumi Sano, Ayaka Saka, Daisuke Watanabe, Masashi Yukawa, Yoshikazu Ohya, Shinichi Morishita:
SCMD: Saccharomyces cerevisiae Morphological Database. 319-322 - Gaëlle Lelandais, Stéphane Le Crom, Frédéric Devaux, Stéphane Vialette, George M. Church, Claude Jacq, Philippe Marc:
yMGV: a cross-species expression data mining tool. 323-325 - Li Li, Jonathan Crabtree, Steve Fischer, Deborah F. Pinney, Christian J. Stoeckert Jr., L. David Sibley, David S. Roos:
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites. 326-328 - Daniela Puiu, Shinichiro Enomoto, Gregory A. Buck, Mitchell S. Abrahamsen, Jessica C. Kissinger:
CryptoDB: the Cryptosporidium genome resource. 329-331 - Lisa Kreppel, Petra Fey, Pascale Gaudet, Eric M. Just, Warren A. Kibbe, Rex L. Chisholm, Alan R. Kimmel:
dictyBase: a new Dictyostelium discoideum genome database. 332-333 - Junichi Watanabe, Yutaka Suzuki, Masahide Sasaki, Sumio Sugano:
Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species. 334-338 - Christiane Hertz-Fowler, Chris S. Peacock, Valerie Wood, Martin Aslett, Arnaud Kerhornou, Paul Mooney, Adrian Tivey, Matthew Berriman, Neil Hall, Kim Rutherford, Julian Parkhill, Alasdair C. Ivens, Marie-Adèle Rajandream, Bart Barrell:
GeneDB: a resource for prokaryotic and eukaryotic organisms. 339-343 - Michael Luchtan, Chetna Warade, D. Brent Weatherly, Wim M. Degrave, Rick L. Tarleton, Jessica C. Kissinger:
TcruziDB: an integrated Trypanosoma cruzi genome resource. 344-346 - Franck Samson, Véronique Brunaud, Sylvain Duchêne, Yannick de Oliveira, Michel Caboche, Alain Lecharny, Sébastien Aubourg:
FLAGdb++: a database for the functional analysis of the Arabidopsis genome. 347-350 - S. Mohseni-Zadeh, Alexandra Louis, Pierre Brézellec, Jean-Loup Risler:
PHYTOPROT: a database of clusters of plant proteins. 351-353 - Qunfeng Dong, Shannon D. Schlueter, Volker Brendel:
PlantGDB, plant genome database and analysis tools. 354-359 - Shu Ouyang, C. Robin Buell:
The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. 360-363 - Manuel Ruiz, Mathieu Rouard, Louis Marie Raboin, Marc Lartaud, Pierre Lagoda, Brigitte Courtois:
TropGENE-DB, a multi-tropical crop information system. 364-367 - Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Lorenz Bülow, Reinhard Hehl:
AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. 368-372 - Heiko Schoof, Rebecca Ernst, Vladimir Nazarov, Lukas Pfeifer, Hans-Werner Mewes, Klaus F. X. Mayer:
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. 373-376 - Wenming Zhao, Jing Wang, Ximiao He, Xiaobing Huang, Yongzhi Jiao, Mingtao Dai, Shulin Wei, Jian Fu, Ye Chen, Xiaoyu Ren, Yong Zhang, Peixiang Ni, Jianguo Zhang, Songgang Li, Jian Wang, Gane Ka-Shu Wong, Hongyu Zhao, Jun Yu, Huanming Yang, Jun Wang:
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. 377-382 - Junshi Yazaki, Keiichi Kojima, Kouji Suzuki, Naoki Kishimoto, Shoshi Kikuchi:
The Rice PIPELINE: a unification tool for plant functional genomics. 383-387 - Setsuko Komatsu, Keiichi Kojima, Kouji Suzuki, Kazuo Ozaki, Kenichi Higo:
Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003. 388-392 - Carolyn J. Lawrence, Qunfeng Dong, Mary L. Polacco, Trent E. Seigfried, Volker Brendel:
MaizeGDB, the community database for maize genetics and genomics. 393-397 - Nadim W. Alkharouf, Benjamin F. Matthews:
SGMD: the Soybean Genomics and Microarray Database. 398-400 - J. E. Mabey, M. J. Anderson, Peter F. Giles, Crispin J. Miller, Terri K. Attwood, Norman W. Paton, Erich Bornberg-Bauer, G. D. Robson, Stephen G. Oliver, David W. Denning:
CADRE: the Central Aspergillus Data REpository. 401-405 - Kristin C. Gunsalus, Wan-Chen Yueh, Philip MacMenamin, Fabio Piano:
RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. 406-410 - Todd W. Harris, Nansheng Chen, Fiona Cunningham, Marcela K. Tello-Ruiz, Igor Antoshechkin, Carol Bastiani, Tamberlyn Bieri, Darin Blasiar, Keith Bradnam, Juancarlos Chan, Chao-Kung Chen, Wen J. Chen, Paul Davis, Eimear Kenny, Ranjana Kishore, Daniel Lawson, Raymond Y. N. Lee, Hans-Michael Müller, Cecilia Nakamura, 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 multi-species resource for nematode biology and genomics. 411-417 - Reed J. Kelso, Michael Buszczak, Ana T. Quiñones, Claudia Castiblanco, Stacy Mazzalupo, Lynn Cooley:
Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster. 418-420 - Jagan Srinivasan, Georg W. Otto, Ulrich Kahlow, Robert Geisler, Ralf J. Sommer:
AppaDB: an AcedB database for the nematode satellite organism Pristionchus pacificus. 421-422 - Todd Wylie, John C. Martin, Michael Dante, Makedonka Dautova Mitreva, Sandra W. Clifton, Asif T. Chinwalla, Robert H. Waterston, Richard K. Wilson, James P. McCarter:
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. 423-426 - John Parkinson, Claire Whitton, Ralf Schmid, Marian Thomson, Mark L. Blaxter:
NEMBASE: a resource for parasitic nematode ESTs. 427-430 - Ida Schomburg, Antje Chang, Christian Ebeling, Marion Gremse, Christian Heldt, Gregor Huhn, Dietmar Schomburg:
BRENDA, the enzyme database: updates and major new developments. 431-433 - Astrid Fleischmann, Michael Darsow, Kirill Degtyarenko, Wolfgang Fleischmann, Sinéad Boyce, Kristian B. Axelsen, Amos Bairoch, Dietmar Schomburg, Keith F. Tipton, Rolf Apweiler:
IntEnz, the integrated relational enzyme database. 434-437 - Cynthia J. Krieger, Peifen Zhang, Lukas A. Mueller, Alfred Wang, Suzanne M. Paley, Martha Arnaud, John Pick, Seung Yon Rhee, Peter D. Karp:
MetaCyc: a multiorganism database of metabolic pathways and enzymes. 438-442 - Christian Lemer, Erick Antezana, Fabian Couche, Frédéric Fays, Xavier Santolaria, Rekin's Janky, Yves Deville, Jean Richelle, Shoshana J. Wodak:
The aMAZE LightBench: a web interface to a relational database of cellular processes. 443-448 - Lukasz Salwínski, Christopher S. Miller, Adam J. Smith, Frank K. Pettit, James U. Bowie, David S. Eisenberg:
The Database of Interacting Proteins: 2004 update. 449-451 - Henning Hermjakob, Luisa Montecchi-Palazzi, Chris Lewington, Sugath Mudali, Samuel Kerrien, Sandra E. Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso Valencia, Hanah Margalit, John Armstrong, Amos Bairoch, Gianni Cesareni, David James Sherman, Rolf Apweiler:
IntAct: an open source molecular interaction database. 452-455 - Ming Chen, Susana Lin, Ralf Hofestädt:
STCDB: Signal Transduction Classification Database. 456-458 - Christophe Andreoli, Holger Prokisch, K. Hörtnagel, Jakob C. Mueller, Martin Münsterkötter, Curt Scharfe, Thomas Meitinger:
MitoP2, an integrated database on mitochondrial proteins in yeast and man. 459-462 - Dawn Cotter, Purnima Guda, Eoin Fahy, Shankar Subramaniam:
MitoProteome: mitochondrial protein sequence database and annotation system. 463-467 - Ewan Birney, T. Daniel Andrews, Paul Bevan, Mario Cáccamo, Graham Cameron, Yuan Chen, Laura Clarke, Guy Coates, Tony Cox, James A. Cuff, Val Curwen, Tim Cutts, Thomas A. Down, Richard Durbin, Eduardo Eyras, Xosé M. Fernández-Suárez, Paul J. Gane, B. Gibbins, James G. R. Gilbert, Martin Hammond, H. Hotz, Vivek Iyer, Andreas Kähäri, Kerstin Jekosch, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Heikki Lehväslaiho, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Glenn Proctor, Mark Rae, Stephen M. J. Searle, Guy Slater, Damian Smedley, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, Abel Ureta-Vidal, Cara Woodwark, Michele E. Clamp, Tim J. P. Hubbard:
Ensembl 2004. 468-470 - Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, Akihiko Konagaya, Christian Schönbach:
FREP: a database of functional repeats in mouse cDNAs. 471-475 - Carol J. Bult, Judith A. Blake, Joel E. Richardson, James A. Kadin, Janan T. Eppig:
The Mouse Genome Database (MGD): integrating biology with the genome. 476-481 - Petr Divina, Jirí Forejt:
The Mouse SAGE Site: database of public mouse SAGE libraries. 482-483 - Hirohide Uenishi, Tomoko Eguchi, Kohei Suzuki, Tetsuya Sawazaki, Daisuke Toki, Hiroki Shinkai, Naohiko Okumura, Noriyuki Hamasima, Takashi Awata:
PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries. 484-488 - Tal Dagan, Rotem Sorek, Eilon Sharon, Gil Ast, Dan Graur:
AluGene: a database of Alu elements incorporated within protein-coding genes. 489-492 - Donna Karolchik, Angela S. Hinrichs, Terrence S. Furey, Krishna M. Roskin, Charles W. Sugnet, David Haussler, W. James Kent:
The UCSC Table Browser data retrieval tool. 493-496 - Suraj Peri, J. Daniel Navarro, Troels Z. Kristiansen, Ramars Amanchy, Vineeth Surendranath, Babylakshmi Muthusamy, T. K. B. Gandhi, K. N. Chandrika, Nandan Deshpande, Shubha Suresh, B. P. Rashmi, K. Shanker, N. Padma, Vidya Niranjan, H. C. Harsha, Naveen Talreja, B. M. Vrushabendra, M. A. Ramya, A. J. Yatish, Mary Joy, H. N. Shivashankar, M. P. Kavitha, Minal Menezes, Dipanwita Roy Chowdhury, Neelanjana Ghosh, R. Saravana, Sreenath Chandran, S. Sujatha Mohan, Chandra Kiran Jonnalagadda, C. K. Prasad, Chandan Kumar-Sinha, Krishna S. Deshpande, Akhilesh Pandey:
Human protein reference database as a discovery resource for proteomics. 497-501 - Reiko Kikuno, Takahiro Nagase, Manabu Nakayama, Hisashi Koga, Noriko Okazaki, Daisuke Nakajima, Osamu Ohara:
HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE. 502-504 - Detlev Bannasch, Alexander Mehrle, Karl-Heinz Glatting, Rainer Pepperkok, Annemarie Poustka, Stefan Wiemann:
LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system. 505-508 - Peter Sperisen, Christian Iseli, Marco Pagni, Brian J. Stevenson, Philipp Bucher, C. Victor Jongeneel:
trome, trEST and trGEN: databases of predicted protein sequences. 509-511 - Paul N. Schofield, Jonathan B. L. Bard, Catherine Booth, Jacques Boniver, Vincenzo Covelli, Philippe Delvenne, Michele Ellender, Wilhelm Engstrom, Wolfgang Goessner, Michael Gruenberger, Heinz Hoefler, John Hopewell, Mariatheresa Mancuso, Carmel Mothersill, Christopher S. Potten, Leticia Quintanilla-Fend, Björn Rozell, Hannu Sariola, John P. Sundberg, Andrew Ward:
Pathbase: a database of mutant mouse pathology. 512-515 - D. Fredman, G. Munns, Daniel Rios, F. Sjöholm, Marianne Siegfried, Boris Lenhard, Heikki Lehväslaiho, Anthony J. Brookes:
HGVbase: a curated resource describing human DNA variation and phenotype relationships. 516-519 - Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Simon Kasif, Jie Liang:
topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. 520-522 - Keiko Akagi, Takeshi Suzuki, Robert M. Stephens, Nancy A. Jenkins, Neal G. Copeland:
RTCGD: retroviral tagged cancer gene database. 523-527 - Bernice R. Packer, Meredith Yeager, Brian Staats, Robert Welch, Andrew Crenshaw, Maureen Kiley, Andrew Eckert, Michael Beerman, Edward Miller, Andrew Bergen, Nathaniel Rothman, Robert Strausberg, Stephen J. Chanock:
SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes. 528-532 - Suisheng Tang, Hao Han, Vladimir B. Bajic:
ERGDB: Estrogen Responsive Genes Database. 533-536 - George P. Patrinos, Belinda Giardine, Cathy Riemer, Webb Miller, David H. K. Chui, Nicholas P. Anagnou, Henri Wajcman, Ross C. Hardison:
Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies. 537-541 - Viviane Praz, Vidhya Jagannathan, Philipp Bucher:
CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. 542-547 - Itoshi Nikaido, Chika Saito, Akiko Wakamoto, Yasuhiro Tomaru, Takahiro Arakawa, Yoshihide Hayashizaki, Yasushi Okazaki:
EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. 548-551 - Axel Visel, Christina Thaller, Gregor Eichele:
GenePaint.org: an atlas of gene expression patterns in the mouse embryo. 552-556 - Christine To, Trevor Epp, Tammy Reid, Qing Lan, Mei Yu, Carol Y. J. Li, Minako Ohishi, Paula Hant, Nora Tsao, Guillermo Casallo, Janet Rossant, Lucy R. Osborne, William L. Stanford:
The Centre for Modeling Human Disease Gene Trap resource. 557-559 - Christa Niederhauser-Wiederkehr, R. Basavaraj, Cyril Sarrauste de Menthière, Leandro Hermida, R. Koch, U. Schlecht, A. Amon, Sophie Brachat, Michael Breitenbach, Peter Briza, Sandrine Caburet, J. Michael Cherry, R. Davis, A. Deutschbauer, H. G. Dickinson, T. Dumitrescu, M. Fellous, A. Goldman, J. Anton Grootegoed, R. Scott Hawley, Ryohei Ishii, B. Jégou, R. J. Kaufman, Franz Klein, N. Lamb, B. Maro, Kim Nasmyth, A. Nicolas, T. Orr-Weaver, Peter Philippsen, Charles Pineau, K. P. Rabitsch, V. Reinke, H. Roest, W. Saunders, M. Schröder, Tim Schedl, M. Siep, A. Villeneuve, Debra J. Wolgemuth, M. Yamamoto, D. Zickler, R. E. Esposito, Michael Primig:
GermOnline, a cross-species community knowledgebase on germ cell differentiation. 560-567 - David P. Hill, Dale A. Begley, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Constance M. Smith, Jon S. Beal, Lori E. Corbani, Judith A. Blake, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald:
The mouse Gene Expression Database (GXD): updates and enhancements. 568-571 - Sung-Ho Goh, Y. Terry Lee, Gerard G. Bouffard, Jeffery L. Miller:
Hembase: browser and genome portal for hematology and erythroid biology. 572-574 - David J. Craigon, Nick James, John Okyere, Janet Higgins, Joan Jotham, Sean T. May:
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. 575-577 - Josephine Chen, Po Zhao, Donald Massaro, Linda B. Clerch, Richard R. Almon, Debra C. DuBois, William J. Jusko, Eric P. Hoffman:
The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. 578-581 - György Babnigg, Carol S. Giometti:
GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes. 582-585 - Manisha Brahmachary, S. P. T. Krishnan, Judice L. Y. Koh, Asif M. Khan, Seng Hong Seah, Tin Wee Tan, Vladimir Brusic, Vladimir B. Bajic:
ANTIMIC: a database of antimicrobial sequences. 586-589 - Zhe Wang, Guangshun Wang:
APD: the Antimicrobial Peptide Database. 590-592 - Lee Whitmore, B. A. Wallace:
The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols. 593-594 - Feng Liang, Udayakumar Matrubutham, Babak Parvizi, Jessica Yen, Daniel Duan, Jyotika Mirchandani, Sandra Hashima, Uyen Nguyen, Eric Ubil, Jake Loewenheim, Xin Yu, Sara Sipes, Wendy Williams, Ling Wang, Robert Bennett, John Carrino:
ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection. 595-599
Volume 32, Web Server Issue, July 2004
- Nicola Harte, Ville Silventoinen, Emmanuel Quevillon, Stephen Robinson, Kimmo Kallio, Xavier Fustero, Pravin Patel, Petteri Jokinen, Rodrigo Lopez:
Public web-based services from the European Bioinformatics Institute. 3-9 - Tien Huynh, Isidore Rigoutsos:
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update. 10-15 - Karsten Hokamp, Kenneth H. Wolfe:
PubCrawler: keeping up comfortably with PubMed and GenBank. 16-19 - Scott D. McGinnis, Thomas L. Madden:
BLAST: at the core of a powerful and diverse set of sequence analysis tools. 20-25 - John B. Spalding, Peter J. Lammers:
BLAST Filter and GraphAlign: rule-based formation and analysis of sets of related DNA and protein sequences. 26-32 - Burkhard Morgenstern:
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. 33-36 - Olivier Poirot, Karsten Suhre, Chantal Abergel, Eamonn O'Toole, Cédric Notredame:
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. 37-40 - Michael Brudno, Rasmus Steinkamp, Burkhard Morgenstern:
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. 41-44 - Ji Qi, Hong Luo, Bailin Hao:
CVTree: a phylogenetic tree reconstruction tool based on whole genomes. 45-47 - Radek Zika, Jan Paces, Adam Pavlícek, Václav Paces:
WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or amino acids sequences. 48-49 - Jahnavi C. Prasad, Sandor Vajda, Carlos J. Camacho:
Consensus alignment server for reliable comparative modeling with distant templates. 50-54 - Masato Ohtsuka, Shohei Horiuchi, Jerzy K. Kulski, Minoru Kimura, Hidetoshi Inoko:
CHOP: visualization of #wobbling' and isolation of highly conserved regions from aligned DNA sequences. 55-58 - William C. Ray:
MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments. 59-63 - Dmitry A. Afonnikov, Nikolay A. Kolchanov:
CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences. 64-68 - Soon-Heng Tan, Zhuo Zhang, See-Kiong Ng:
ADVICE: Automated Detection and Validation of Interaction by Co-Evolution. 69-72 - Zhuo Zhang, See-Kiong Ng:
InterWeaver: interaction reports for discovering potential protein interaction partners with online evidence. 73-75 - Darby Tien-Hao Chang, Chien-Yu Chen, Wen-Chin Chung, Yen-Jen Oyang, Hsueh-Fen Juan, Hsuan-Cheng Huang:
ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures. 76-82 - Brian P. Kelley, Bingbing Yuan, Fran Lewitter, Roded Sharan, Brent R. Stockwell, Trey Ideker:
PathBLAST: a tool for alignment of protein interaction networks. 83-88 - Kyungsook Han, Byong-Hyon Ju, Haemoon Jung:
WebInterViewer: visualizing and analyzing molecular interaction networks. 89-95 - Stephen R. Comeau, David W. Gatchell, Sandor Vajda, Carlos J. Camacho:
ClusPro: a fully automated algorithm for protein-protein docking. 96-99 - Chittibabu Guda, Sifang Lu, Eric D. Scheeff, Philip E. Bourne, Ilya N. Shindyalov:
CE-MC: a multiple protein structure alignment server. 100-103 - Shandar Ahmad, Akinori Sarai:
Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins. 104-107 - Kirill Rotmistrovsky, Wonhee Jang, Gregory D. Schuler:
A web server for performing electronic PCR. 108-112 - Andreas Henschel, Frank Buchholz, Bianca Habermann:
DEQOR: a web-based tool for the design and quality control of siRNAs. 113-120 - Peter Dudek, Didier Picard:
TROD: T7 RNAi Oligo Designer. 121-123 - Yuki Naito, Tomoyuki Yamada, Kumiko Ui-Tei, Shinichi Morishita, Kaoru Saigo:
siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference. 124-129 - Bingbing Yuan, Robert Latek, Markus Hossbach, Thomas Tuschl, Fran Lewitter:
siRNA Selection Server: an automated siRNA oligonucleotide prediction server. 130-134 - Ye Ding, Chi Yu Chan, Charles E. Lawrence:
Sfold web server for statistical folding and rational design of nucleic acids. 135-141 - Hélène Touzet, Olivier Perriquet:
CARNAC: folding families of related RNAs. 142-145 - Jianhua Ruan, Gary D. Stormo, Weixiong Zhang:
ILM: a web server for predicting RNA secondary structures with pseudoknots. 146-149 - Xiaomin Ying, Hong Luo, Jingchu Luo, Wuju Li:
RDfolder: a web server for prediction of RNA secondary structure. 150-153 - Peter Bengert, Thomas Dandekar:
Riboswitch finder tool for identification of riboswitch RNAs. 154-159 - André Lambert, Jean-Fred Fontaine, Matthieu Legendre, Fabrice Leclerc, Emmanuelle Permal, François Major, Harald Putzer, Olivier Delfour, Bernard Michot, Daniel Gautheret:
The ERPIN server: an interface to profile-based RNA motif identification. 160-165 - Sònia Casillas, Antonio Barbadilla:
PDA: a pipeline to explore and estimate polymorphism in large DNA databases. 166-169 - Stefan Weckx, Peter De Rijk, Christine Van Broeckhoven, Jurgen Del-Favero:
SNPbox: web-based high-throughput primer design from gene to genome. 170-172 - Wolfgang Helmberg, Raymond Dunivin, Michael Feolo:
The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences. 173-175 - Jean-Marie Rouillard, Woonghee Lee, Gilles Truan, Xiaolian Gao, Xiaochuan Zhou, Erdogan Gulari:
Gene2Oligo: oligonucleotide design for in vitro gene synthesis. 176-180 - Namshin Kim, Seokmin Shin, Sanghyuk Lee:
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences. 181-186 - William G. Fairbrother, Gene W. Yeo, Rufang Yeh, Paul Goldstein, Matthew Mawson, Phillip A. Sharp, Christopher B. Burge:
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. 187-190 - Anason S. Halees, Zhiping Weng:
PromoSer: improvements to the algorithm, visualization and accessibility. 191-194 - Wynand Alkema, Öjvind Johansson, Jens Lagergren, Wyeth W. Wasserman:
MSCAN: identification of functional clusters of transcription factor binding sites. 195-198 - Giulio Pavesi, Paolo Mereghetti, Giancarlo Mauri, Graziano Pesole:
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. 199-203 - Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, Xiaole Shirley Liu:
A suite of web-based programs to search for transcriptional regulatory motifs. 204-207 - Dmitry Yu. Oshchepkov, Evgenii E. Vityaev, Dmitry A. Grigorovich, Elena V. Ignatieva, Tamara M. Khlebodarova:
SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition. 208-212 - Peter M. Haverty, Martin C. Frith, Zhiping Weng:
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. 213-216 - Gabriela G. Loots, Ivan Ovcharenko:
rVISTA 2.0: evolutionary analysis of transcription factor binding sites. 217-221 - Matti Kankainen, Liisa Holm:
POBO, transcription factor binding site verification with bootstrapping. 222-229 - Hong Pan, Li Zuo, Vidhu Choudhary, Zhuo Zhang, Shoi Houi Leow, Fui Teen Chong, Yingliang Huang, Victor Wui Siong Ong, Bijayalaxmi Mohanty, Sin Lam Tan, S. P. T. Krishnan, Vladimir B. Bajic:
Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining. 230-234 - Zhenjun Hu, Yutao Fu, Anason S. Halees, Szymon M. Kielbasa, Zhiping Weng:
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. 235-241 - Lucía Conde, Juan M. Vaquerizas, Javier Santoyo, Fátima Al-Shahrour, Sergio Ruiz-Llorente, Mercedes Robledo, Joaquín Dopazo:
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. 242-248 - Albin Sandelin, Wyeth W. Wasserman, Boris Lenhard:
ConSite: web-based prediction of regulatory elements using cross-species comparison. 249-252 - Roded Sharan, Asa Ben-Hur, Gabriela G. Loots, Ivan Ovcharenko:
CREME: Cis-Regulatory Module Explorer for the human genome. 253-256 - Vinsensius B. Vega, Dhinoth Kumar Bangarusamy, Lance D. Miller, Edison T. Liu, Chin-Yo Lin:
BEARR: Batch Extraction and Analysis of cis-Regulatory Regions. 257-260 - Klaus Karl Lohmann, Claus-Wilhelm von der Lieth:
GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates. 261-266 - Kiyoko F. Aoki, Atsuko Yamaguchi, Nobuhisa Ueda, Tatsuya Akutsu, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa:
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. 267-272 - Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, Inna Dubchak:
VISTA: computational tools for comparative genomics. 273-279 - Ivan Ovcharenko, Marcelo A. Nobrega, Gabriela G. Loots, Lisa Stubbs:
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. 280-286 - José L. Oliver, Pedro Carpena, Michael Hackenberg, Pedro Bernaola-Galván:
IsoFinder: computational prediction of isochores in genome sequences. 287-292 - Marco Masseroli, Dario Martucci, Francesco Pinciroli:
GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining. 293-300 - Jan Krüger, Alexander Sczyrba, Stefan Kurtz, Robert Giegerich:
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. 301-304 - Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Burkhard Morgenstern:
AGenDA: gene prediction by cross-species sequence comparison. 305-308 - Mario Stanke, Rasmus Steinkamp, Stephan Waack, Burkhard Morgenstern:
AUGUSTUS: a web server for gene finding in eukaryotes. 309-312 - Detlef Groth, Hans Lehrach, Steffen Hennig:
GOblet: a platform for Gene Ontology annotation of anonymous sequence data. 313-317 - Sailu Yellaboina, Jayashree Seshadri, M. Senthil Kumar, Akash Ranjan:
PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes. 318-320 - Burkhard Rost, Guy Yachdav, Jinfeng Liu:
The PredictProtein server. 321-326 - Aron Marchler-Bauer, Stephen H. Bryant:
CD-Search: protein domain annotations on the fly. 327-331 - Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Laurent Falquet:
MyHits: a new interactive resource for protein annotation and domain identification. 332-335 - François Enault, Karsten Suhre, Olivier Poirot, Chantal Abergel, Jean-Michel Claverie:
Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis. 336-339 - Richard D. LeDuc, Gregory K. Taylor, Yong-Bin Kim, Thomas E. Januszyk, Lee H. Bynum, Joseph V. Sola, John S. Garavelli, Neil L. Kelleher:
ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry. 340-345 - Victor G. Levitsky:
RECON: a program for prediction of nucleosome formation potential. 346-349 - Johann Lenffer, Paulo Lai, Wafaa El Mejaber, Asif M. Khan, Judice L. Y. Koh, Paul T. J. Tan, Seng Hong Seah, Vladimir Brusic:
CysView: protein classification based on cysteine pairing patterns. 350-355 - Lesheng Kong, Bernett Teck Kwong Lee, Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan:
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins. 356-359 - Brian D. O'Connor, Todd O. Yeates:
GDAP: a web tool for genome-wide protein disulfide bond prediction. 360-364 - Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Brett Poulin, Roman Eisner, Zhiyong Lu, John Anvik, Cam Macdonell, Alona Fyshe, David Meeuwis:
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. 365-371 - Chittibabu Guda, Purnima Guda, Eoin Fahy, Shankar Subramaniam:
MITOPRED: a web server for the prediction of mitochondrial proteins. 372-374 - Karsten Hiller, Andreas Grote, Maurice Scheer, Richard Münch, Dieter Jahn:
PrediSi: prediction of signal peptides and their cleavage positions. 375-379 - Panagiotis K. Papasaikas, Pantelis G. Bagos, Zoi I. Litou, Vasilis J. Promponas, Stavros J. Hamodrakas:
PRED-GPCR: GPCR recognition and family classification server. 380-382 - Manoj Bhasin, G. P. S. Raghava:
GPCRpred: an SVM-based method for prediction of families and subfamilies of G-protein coupled receptors. 383-389 - Masafumi Arai, Hironori Mitsuke, Masami Ikeda, Jun-Xiong Xia, Takashi Kikuchi, Masanobu Satake, Toshio Shimizu:
ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. 390-393 - Frode S. Berven, Kristian Flikka, Harald B. Jensen, Ingvar Eidhammer:
BOMP: a program to predict integral ?barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. 394-399 - Pantelis G. Bagos, Theodore Liakopoulos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas:
PRED-TMBB: a web server for predicting the topology of ?barrel outer membrane proteins. 400-404 - Mohd. Zeeshan Ansari, Gitanjali Yadav, Rajesh S. Gokhale, Debasisa Mohanty:
NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. 405-413 - Manoj Bhasin, G. P. S. Raghava:
ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. 414-419 - Yutao Fu, Martin C. Frith, Peter M. Haverty, Zhiping Weng:
MotifViz: an analysis and visualization tool for motif discovery. 420-423 - Olga V. Kalinina, Pavel S. Novichkov, Andrey A. Mironov, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova:
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. 424-428 - Cédric Muller, Mathieu Denis, Laurent Gentzbittel, Thomas Faraut:
The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species. 429-434 - Véronique Giudicelli, Denys Chaume, Marie-Paule Lefranc:
IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor VJ and VDJrearrangement analysis. 435-440 - Kei-Hoi Cheung, Janet Hager, Deyun Pan, Ranjana Srivastava, Shrikant M. Mane, Yuli Li, Perry L. Miller, Kenneth R. Williams:
KARMA: a web server application for comparing and annotating heterogeneous microarray platforms. 441-444 - Lars Juhl Jensen, Julien Lagarde, Christian von Mering, Peer Bork:
ArrayProspector: a web resource of functional associations inferred from microarray expression data. 445-448 - Purvesh Khatri, Pratik Bhavsar, Gagandeep Bawa, Sorin Draghici:
Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. 449-456 - Karsten Hokamp, Fiona M. Roche, Michael Acab, Marc-Etienne Rousseau, Byron Kuo, David L. Goode, Dana Aeschliman, Jenny Bryan, Lorne A. Babiuk, Robert E. W. Hancock, Fiona S. L. Brinkman:
ArrayPipe: a flexible processing pipeline for microarray data. 457-459 - Hee-Joon Chung, Mingoo Kim, Chan Hee Park, Jihoon Kim, Ju Han Kim:
ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. 460-464 - Misha Kapushesky, Patrick Kemmeren, Aedín C. Culhane, Steffen Durinck, Jan Ihmels, Christine Körner, Meelis Kull, Aurora Torrente, Ugis Sarkans, Jaak Vilo, Alvis Brazma:
Expression Profiler: next generation - an online platform for analysis of microarray data. 465-470 - Fiona M. Roche, Karsten Hokamp, Michael Acab, Lorne A. Babiuk, Robert E. W. Hancock, Fiona S. L. Brinkman:
ProbeLynx: a tool for updating the association of microarray probes to genes. 471-474 - Suresh Karanam, Carlos Sanchez Moreno:
CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets. 475-484 - Javier Herrero, Juan M. Vaquerizas, Fátima Al-Shahrour, Lucía Conde, Álvaro Mateos, Javier Santoyo, Ramón Díaz-Uriarte, Joaquín Dopazo:
New challenges in gene expression data analysis and the extended GEPAS. 485-491 - Stefano Volinia, Rita Evangelisti, Francesca Francioso, Diego Arcelli, Massimo Carella, Paolo Gasparini:
GOAL: automated Gene Ontology analysis of expression profiles. 492-499 - Matthias Heinig, Dmitrij Frishman:
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. 500-502 - Maxim Shatsky, Oranit Dror, Dina Schneidman-Duhovny, Ruth Nussinov, Haim J. Wolfson:
BioInfo3D: a suite of tools for structural bioinformatics. 503-507 - R. Gautier, Anne-Claude Camproux, Pierre Tufféry:
SCit: web tools for protein side chain conformation analysis. 508-511 - Alexander V. Diemand, Holger Scheib:
iMolTalk: an interactive, internet-based protein structure analysis server. 512-516 - Rajesh Nair, Burkhard Rost:
LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. 517-521 - Jun-tao Guo, Kyle Ellrott, Won Jae Chung, Dong Xu, Sergei Passovets, Ying Xu:
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. 522-525 - David E. Kim, Dylan Chivian, David Baker:
Protein structure prediction and analysis using the Robetta server. 526-531 - Andrew E. Torda, James B. Procter, Thomas Huber:
Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. 532-535 - Jessica Shapiro, Douglas L. Brutlag:
FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web. 536-541 - Giridhar Chukkapalli, Chittibabu Guda, Shankar Subramaniam:
SledgeHMMER: a web server for batch searching the Pfam database. 542-544 - Frédéric Guyon, Anne-Claude Camproux, Joëlle Hochez, Pierre Tufféry:
SA-Search: a web tool for protein structure mining based on a Structural Alphabet. 545-548 - Vladimir A. Ivanisenko, Sergey S. Pintus, Dmitry A. Grigorovich, Nikolay A. Kolchanov:
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. 549-554 - T. Andrew Binkowski, Patrick Freeman, Jie Liang:
pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. 555-558 - Balvinder Singh:
PepBuild: a web server for building structure data of peptides/proteins. 559-561 - Fan Xue, Zhong Gu, Jin-An Feng:
LINKER: a web server to generate peptide sequences with extended conformation. 562-565 - William J. Salerno, Samuel M. Seaver, Brian R. Armstrong, Ishwar Radhakrishnan:
MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data. 566-568 - Jinfeng Liu, Burkhard Rost:
CHOP: parsing proteins into structural domains. 569-571 - Chi-Ren Shyu, Pin-Hao Chi, Grant J. Scott, Dong Xu:
ProteinDBS: a real-time retrieval system for protein structure comparison. 572-575 - Krzysztof Ginalski, Marcin von Grotthuss, Nick V. Grishin, Leszek Rychlewski:
Detecting distant homology with Meta-BASIC. 576-581 - Yuzhen Ye, Adam Godzik:
FATCAT: a web server for flexible structure comparison and structure similarity searching. 582-585 - Joanna M. Sasin, Janusz M. Bujnicki:
COLORADO3D, a web server for the visual analysis of protein structures. 586-589 - Rajarshi Maiti, Gary H. Van Domselaar, Haiyan Zhang, David S. Wishart:
SuperPose: a simple server for sophisticated structural superposition. 590-594 - Goran Neshich, Walter Rocchia, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Christian Baudet, Ivan P. Pinto, Arnaldo J. Montagner, Juliana F. Palandrani, João N. Krauchenco, Renato C. Torres, Savio Souza, Roberto C. Togawa, Roberto H. Higa:
JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. 595-601 - Anirban Bhaduri, Ganesan Pugalenthi, Nitin Gupta, Ramanathan Sowdhamini:
iMOT: an interactive package for the selection of spatially interacting motifs. 602-605 - Jean-Baptiste Claude, Karsten Suhre, Cédric Notredame, Jean-Michel Claverie, Chantal Abergel:
CaspR: a web server for automated molecular replacement using homology modelling. 606-609 - Karsten Suhre, Yves-Henri Sanejouand:
ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. 610-614 - Ian W. Davis, Laura Weston Murray, Jane S. Richardson, David C. Richardson:
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. 615-619 - Neil Maudling, Terri K. Attwood:
FAN: fingerprint analysis of nucleotide sequences. 620-623 - Tiziana Castrignanò, Alessandro Canali, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Graziano Pesole:
CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison. 624-627 - Yuri L. Orlov, Vladimir N. Potapov:
Complexity: an internet resource for analysis of DNA sequence complexity. 628-633 - Sven Mika, Burkhard Rost:
NLProt: extracting protein names and sequences from papers. 634-637 - Brian D. Halligan, Victor Ruotti, Weihong Jin, Scott Laffoon, Simon N. Twigger, Edward A. Dratz:
ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels. 638-644 - P. Selvarani, V. Shanthi, C. K. Rajesh, S. Saravanan, Krishna Sekar:
BSDD: Biomolecules Segment Display Device's web-based interactive display tool. 645-648 - Jeff Reneker, Chi-Ren Shyu, Peiyu Zeng, Joseph C. Polacco, Walter Gassmann:
ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval. 649-653 - Mikhail Rozanov, Uwe Plikat, Colombe Chappey, Andrey Kochergin, Tatiana A. Tatusova:
A web-based genotyping resource for viral sequences. 654-659 - Xiaoli Dong, Paul Stothard, Ian J. Forsythe, David S. Wishart:
PlasMapper: a web server for drawing and auto-annotating plasmid maps. 660-664 - Todd J. Dolinsky, Jens Erik Nielsen, James Andrew McCammon, Nathan A. Baker:
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. 665-667 - Lee Whitmore, B. A. Wallace:
DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data. 668-673 - Jorge Fernandez-de-Cossío, Luis Javier González, Yoshinori Satomi, Lazaro Betancourt, Yassel Ramos, Vivian Huerta, Abel Amaro, Vladimir Besada, Gabriel Padron, Naoto Minamino, Toshifumi Takao:
Isotopica: a tool for the calculation and viewing of complex isotopic envelopes. 674-678 - Zhi Wei Cao, Ying Xue, Lianyi Han, B. Xie, H. Zhou, C. J. Zheng, Honghuang Lin, Yuzong Chen:
MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids. 679-685
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