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ORCIDNucleic Acids Research, Volume 31
Volume 31, Number 1, January 2003
- Andreas D. Baxevanis:
The Molecular Biology Database Collection: 2003 update. 1-12 - Satoru Miyazaki, Hideaki Sugawara, Takashi Gojobori, Yoshio Tateno:
DNA Data Bank of Japan (DDBJ) in XML. 13-16 - Guenter Stoesser, Wendy Baker, Alexandra van den Broek, Maria Garcia-Pastor, Carola Kanz, Tamara Kulikova, Rasko Leinonen
, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Francesco Nardone, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan:
The EMBL Nucleotide Sequence Database: major new developments. 17-22 - Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, David L. Wheeler:
GenBank. 23-27 - David L. Wheeler, Deanna M. Church, Scott Federhen, Alex E. Lash, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tatiana A. Tatusova, Lukas Wagner:
Database resources of the National Center for Biotechnology. 28-33 - Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott:
NCBI Reference Sequence Project: update and current status. 34-37 - Michele E. Clamp, T. Daniel Andrews, Daniel Barker, Paul Bevan, Graham Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas A. Down, Richard Durbin, Eduardo Eyras, James G. R. Gilbert, Martin Hammond, Tim J. P. Hubbard, Arek Kasprzyk, Damian Keefe, Heikki Lehväslaiho, Vivek Iyer, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Alistair G. Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, Ewan Birney:
Ensembl 2002: accommodating comparative genomics. 38-42 - Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola J. Mulder, Claire O'Donovan, Helen E. Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron:
The European Bioinformatics Institute's data resources. 43-50 - Donna Karolchik, Robert Baertsch, Mark Diekhans, Terrence S. Furey, Angela S. Hinrichs, Yontao Lu, Krishna M. Roskin, Matt Schwartz, Charles W. Sugnet, Daryl J. Thomas, Ryan J. Weber, David Haussler, W. James Kent:
The UCSC Genome Browser Database. 51-54 - Christoph Dieterich, Haiyan Wang, Katja Rateitschak, Hannes Luz, Martin Vingron:
CORG: a database for COmparative Regulatory Genomics. 55-57 - Ikuo Uchiyama:
MBGD: microbial genome database for comparative analysis. 58-62 - Magalie Leveugle, Karine Prat, Nadine Perrier, Daniel Birnbaum, François Coulier:
ParaDB: a tool for paralogy mapping in vertebrate genomes. 63-67 - Alvis Brazma, Helen E. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Jaak Vilo, Niran Abeygunawardena, Ele Holloway, Misha Kapushesky, Patrick Kemmeren, Gonzalo Garcia Lara, Ahmet Oezcimen, Philippe Rocca-Serra, Susanna-Assunta Sansone:
ArrayExpress - a public repository for microarray gene expression data at the EBI. 68-71 - Thorsten Henrich, Mirana Ramialison, Rebecca Quiring, Beate Wittbrodt, Makoto Furutani-Seiki, Joachim Wittbrodt, Hisato Kondoh:
MEPD: a Medaka gene expression pattern database. 72-74 - Céline Amoreira, Winfried Hindermann, Christoph Grunau:
An improved version of the DNA methylation database (MethDB). 75-77 - Kevin Roberg-Perez, Corey M. Carlson, David A. Largaespada:
MTID: a database of Sleeping Beauty transposon insertions in mice. 78-81 - Guoying Liu, Ann E. Loraine, Ron Shigeta, Melissa S. Cline, Jill Cheng, Venu Valmeekam, Shaw Sun, David Kulp, Michael A. Siani-Rose:
NetAffx: Affymetrix probesets and annotations. 82-86 - Pavel V. Baranov, Olga L. Gurvich, Andrew W. Hammer, Raymond F. Gesteland, John F. Atkins:
RECODE 2003. 87-89 - Iris Tzafrir, Allan Dickerman, Olga Brazhnik, Quoc Nguyen, John McElver, Catherine Frye, David Patton, David Meinke:
The Arabidopsis SeedGenes Project. 90-93 - Jeremy Gollub, Catherine A. Ball, Gail Binkley, Janos Demeter, David B. Finkelstein, Joan M. Hebert, Tina Hernandez-Boussard, Heng Jin, Miroslava Kaloper, John C. Matese, Mark Schroeder, Patrick O. Brown, David Botstein, Gavin Sherlock:
The Stanford Microarray Database: data access and quality assessment tools. 94-96 - Mathias Krull, Nico Voss, Claudia Choi, Susanne Pistor, Anatolij Potapov, Edgar Wingender:
TRANSPATH: An integrated database on signal transduction and a tool for array analysis. 97-100 - Christopher J. Lee, Levan Atanelov, Barmak Modrek, Yi Xing:
ASAP: the Alternative Splicing Annotation Project. 101-105 - Vattipally B. Sreenu, Vishwanath Alevoor, Javaregowda Nagaraju, Hampapathalu A. Nagarajaram:
MICdb: database of prokaryotic microsatellites. 106-108 - William C. Ray, Charles J. Daniels:
PACRAT: a database and analysis system for archaeal and bacterial intergenic sequence features. 109-113 - Ilham A. Shahmuradov, Alex J. Gammerman, John M. Hancock, Peter M. Bramley, Victor V. Solovyev:
PlantProm: a database of plant promoter sequences. 114-117 - Julia V. Ponomarenko, Tatyana I. Merkulova, Galina Orlova, Oleg N. Fokin, Elena Gorshkova, Anatoly S. Frolov, Vadim P. Valuev, Mikhail P. Ponomarenko:
rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation. 118-121 - Filip Pattyn, Frank Speleman, Anne De Paepe, Jo Vandesompele:
RTPrimerDB: the Real-Time PCR primer and probe database. 122-123 - Gudmundur A. Thorisson, Lincoln Stein:
The SNP Consortium website: past, present and future. 124-127 - Stephen Rudd, Hans-Werner Mewes, Klaus F. X. Mayer:
Sputnik: a database platform for comparative plant genomics. 128-132 - Todd W. Harris, Raymond Y. N. Lee, Erich M. Schwarz, Keith Bradnam, Daniel Lawson, Wen J. Chen, Darin Blasiar, Eimear Kenny, Fiona Cunningham, Ranjana Kishore, Juancarlos Chan, Hans-Michael Müller, Andrei Petcherski, Gudmundur A. Thorisson, Allen Day, Tamberlyn Bieri, Anthony Rogers, Chao-Kung Chen, John Spieth, Paul W. Sternberg, Richard Durbin, Lincoln D. Stein:
WormBase: a cross-species database for comparative genomics. 133-137 - Emmanuelle Karsenty, Emmanuel Barillot, Gwenola Tosser-Klopp, Yvette Lahbib-Mansais, Denis Milan, Francois Hatey, Susanna Cirera, Milena Sawera, Claus B. Jørgensen, Bhanu Chowdhary, Merete Fredholm, Klaus Wimmers, Siriluck Ponsuksili, Roberta Davoli, Luca Fontanesi, Silvia Braglia, Paolo Zambonelli, Daniele Bigi, Stefan Neuenschwander, Joël Gellin:
The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa). 138-141 - Marilyn Safran, Vered Chalifa-Caspi, Orit Shmueli, Tsviya Olender, Michal Lapidot, Naomi Rosen, Michael Shmoish, Yakov Peter, Gustavo Glusman, Ester Feldmesser, Avital Adato, Inga Peter, Miriam Khen, Tal Atarot, Yoram Groner, Doron Lancet:
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE. 142-146 - Jeremy D. Glasner, Paul Liss, Guy Plunkett III, Aaron E. Darling, Tejasvini Prasad, Michael Rusch, Alexis Byrnes, Michael K. Gilson, Bryan S. Biehl, Frederick R. Blattner, Nicole T. Perna:
ASAP, a systematic annotation package for community analysis of genomes. 147-151 - John W. Urbance, James R. Cole, Paul Saxman, James M. Tiedje:
BSD: the Biodegradative Strain Database. 152-155 - Mark L. Crowe, Carine Serizet, Vincent Thareau, Sébastien Aubourg, Pierre Rouzé, Pierre Hilson, Jim Beynon, Peter Weisbeek, Paul van Hummelen, Philippe Reymond, Javier Paz-Ares, Wilfried Nietfeld, Martin Trick:
CATMA: a complete Arabidopsis GST database. 156-158 - Joseph F. Ryan, John R. Finnerty:
CnidBase: The Cnidarian Evolutionary Genomics Database. 159-163 - Ross A. Overbeek, Niels Larsen, Theresa Walunas, Mark D'Souza, Gordon D. Pusch, Evgeni Selkov Jr., Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vassieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, Nikos Kyrpides:
The ERGOTM genome analysis and discovery system. 164-171 - Emmet A. O'Brien, Elarbi Badidi, Ania Barbasiewicz, Cristina deSousa, B. Franz Lang, Gertraud Burger:
GOBASE - a database of mitochondrial and chloroplast information. 176-178 - Delphine Samson, Fabrice Legeai, Emmanuelle Karsenty, Sébastien Reboux, Jean-Baptiste Veyrieras, Jeremy Just, Emmanuel Barillot:
GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics. 179-182 - David E. Matthews, Victoria L. Carollo, Gerard R. Lazo, Olin D. Anderson:
GrainGenes, the genome database for small-grain crops. 183-186 - Santiago Garcia-Vallvé, Eduard Guzmán, M. A. Montero, Antoni Romeu:
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. 187-189 - Wojciech M. Karlowski, Heiko Schoof, Vijayalakshmi Janakiraman, Volker Stümpflen, Klaus F. X. Mayer:
MOsDB: an integrated information resource for rice genomics. 190-192 - Judith A. Blake, Joel E. Richardson, Carol J. Bult, James A. Kadin, Janan T. Eppig:
MGD: the Mouse Genome Database. 193-195 - Anne-Françoise J. Lamblin, John A. Crow, James E. Johnson, Kevin A. T. Silverstein, Timothy M. Kunau, Alan Kilian, Diane Benz, Martina V. Stromvik, Gabriella Endré, Kathryn A. VandenBosch, Douglas R. Cook, Nevin D. Young, Ernest F. Retzel:
MtDB: a database for personalized data mining of the model legume Medicago truncatula transcriptome. 196-201 - Daniel Jameson, Andrew P. Gibson, Cendrine Hudelot, Paul G. Higgs:
OGRe: a relational database for comparative analysis of mitochondrial genomes. 202-206 - Dmitrij Frishman, Martin Mokrejs, Denis Kosykh, Gabi Kastenmüller, Grigory Kolesov, Igor Zubrzycki, Christian Gruber, Birgitta Geier, Andreas Kaps, Kaj Albermann, Andreas Volz, Christian Wagner, Matthias Fellenberg, Klaus Heumann, Hans-Werner Mewes:
The PEDANT genome database. 207-211 - Amit Bahl, Brian P. Brunk, Jonathan Crabtree, Martin J. Fraunholz, Bindu Gajria, Gregory R. Grant, Hagai Ginsburg, Dinesh Gupta, Jessica C. Kissinger, Philip Labo, Li Li, Matthew D. Mailman, Arthur J. Milgram, David S. Pearson, David S. Roos, Jonathan Schug, Christian J. Stoeckert Jr., Patricia L. Whetzel:
PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. 212-215 - Shuai Weng, Qing Dong, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Laurie Issel-Tarver, Anand Sethuraman, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Christopher Lane, Mark Schroeder, David Botstein, J. Michael Cherry:
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. 216-218 - Maximilian Diehn, Gavin Sherlock, Gail Binkley, Heng Jin, John C. Matese, Tina Hernandez-Boussard, Christian A. Rees, J. Michael Cherry, David Botstein, Patrick O. Brown, Ash A. Alizadeh:
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. 219-223 - Seung Yon Rhee, William D. Beavis, Tanya Z. Berardini, Guanghong Chen, David A. Dixon, Aisling Doyle, Margarita Garcia-Hernandez, Eva Huala, Gabriel Lander, Mary Montoya, Neil Miller, Lukas A. Mueller, Suparna Mundodi, Leonore Reiser, Julie Tacklind, Dan C. Weems, Yihe Wu, Iris Xu, Daniel Yoo, Jungwon Yoon, Peifen Zhang:
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. 224-228 - Qiaoping Yuan, Shu Ouyang, Jia Liu, Bernard B. Suh, Foo Cheung, Razvan Sultana, Daniel Lee, John Quackenbush, C. Robin Buell:
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. 229-233 - Jessica C. Kissinger, Bindu Gajria, Li Li, Ian T. Paulsen, David S. Roos:
ToxoDB: accessing the Toxoplasma gondii genome. 234-236 - Philippe Vaglio, Philippe Lamesch, Jérôme Reboul, Jean-François Rual, Monica Martinez, David E. Hill, Marc Vidal:
WorfDB: the Caenorhabditis elegans ORFeome Database. 237-240 - Judy Sprague, Dave Clements, Tom Conlin, Pat Edwards, Ken Frazer, Kevin Schaper, Erik Segerdell, Peiran Song, Brock Sprunger, Monte Westerfield:
The Zebrafish Information Network (ZFIN): the zebrafish model organism database. 241-243 - Qunfeng Dong, Laura Roy, Michael Freeling, Virginia Walbot, Volker Brendel:
ZmDB, an integrated database for maize genome research. 244-247 - Gary D. Bader, Doron Betel, Christopher W. V. Hogue:
BIND: the Biomolecular Interaction Network Database. 248-250 - See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan, Kui Lin:
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. 251-254 - Zhi Liang Ji, X. Chen, C. J. Zheng, L. X. Yao, L. Y. Han, Wee Kiang Yeo, P. C. Chung, H. S. Puy, Y. T. Tay, A. Muhammad, Yu Zong Chen:
KDBI: Kinetic Data of Bio-molecular Interactions database. 255-257 - Christian von Mering, Martijn A. Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, Berend Snel:
STRING: a database of predicted functional associations between proteins. 258-261 - Lynda B. M. Ellis, Bo Kyeng Hou, Wenjun Kang, Lawrence P. Wackett:
The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining. 262-265 - Richard Münch, Karsten Hiller, Heiko Barg, Dana Heldt, Simone Linz, Edgar Wingender, Dieter Jahn:
PRODORIC: prokaryotic database of gene regulation. 266-269 - Haseena Rajeevan, Michael V. Osier, Kei-Hoi Cheung, H. Deng, L. Druskin, R. Heinzen, Judith R. Kidd, S. Stein, Andrew J. Pakstis, Nick P. Tosches, C.-C. Yeh, Perry L. Miller, Kenneth K. Kidd:
ALFRED: the ALelle FREquency Database. Update. 270-271 - Jean-Loup Huret, Philippe Dessen, Alain Bernheim:
Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003. 272-274 - Frank W. Nicholas:
Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals. 275-277 - Doug Stryke, Michiko Kawamoto, Conrad C. Huang, Susan J. Johns, Leslie A. King, Courtney A. Harper, Elaine C. Meng, Roy E. Lee, Alice Yee, Larry L'Italien, Pao-Tien Chuang, Stephen G. Young, William C. Skarnes, Patricia C. Babbitt, Thomas E. Ferrin:
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. 278-281 - Cyril Sarrauste de Menthière, Stéphane Terrière, Denis Pugnère, Manuel Ruiz, Jacques Demaille, Isabelle Touitou:
INFEVERS: the Registry for FMF and hereditary inflammatory disorders mutations. 282-285 - Denis Pugnère, Manuel Ruiz, Cyril Sarrauste de Menthière, Benjamin Masdoua, Jacques Demaille, Isabelle Touitou:
The MetaFMF website: a high quality tool for meta-analysis of FMF. 286-290 - Long-Cheng Li, Hong Zhao, Hiroaki Shiina, Christopher J. Kane, Rajvir Dahiya:
PGDB: a curated and integrated database of genes related to the prostate. 291-293 - Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E. Cohen, Gerrit Vriend:
GPCRDB information system for G protein-coupled receptors. 294-297 - Soo-Yon Rhee, Matthew J. Gonzales, Rami Kantor, Bradley J. Betts, Jaideep Ravela, Robert W. Shafer:
Human immunodeficiency virus reverse transcriptase and protease sequence database. 298-303 - Sharmila Banerjee-Basu, Travis Moreland, Benjamin J. Hsu, Kenneth L. Trout, Andreas D. Baxevanis:
The Homeodomain Resource: 2003 update. 304-306 - Marie-Paule Lefranc:
IMGT, the international ImMunoGeneTics database®. 307-310 - James Robinson, Matthew J. Waller, Peter Parham, Natasja de Groot, Ronald Bontrop, Lorna J. Kennedy, Peter Stoehr, Steven G. E. Marsh:
IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. 311-314 - Nicola J. Mulder, Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, Philipp Bucher, Richard R. Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Laurent Falquet, Wolfgang Fleischmann, Sam Griffiths-Jones, Daniel H. Haft, Nicola Harte, Nicolas Hulo, Daniel Kahn, Alexander Kanapin, Maria Krestyaninova, Rodrigo Lopez, Ivica Letunic, David Lonsdale, Ville Silventoinen, Sandra E. Orchard, Marco Pagni, David Peyruc, Chris P. Ponting, Jeremy D. Selengut, Florence Servant, Christian J. A. Sigrist, Robert Vaughan, Evgeni M. Zdobnov:
The InterPro Database, 2003 brings increased coverage and new features. 315-318 - Markus Fischer, Jürgen Pleiss:
The Lipase Engineering Database: a navigation and analysis tool for protein families. 319-321 - Marco Sardiello, Flavio Licciulli, Domenico Catalano, Marcella Attimonelli, Corrado Caggese:
MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion. 322-324 - Ryan Lister, Monika W. Murcha, James Whelan:
The Mitochondrial Protein Import Machinery of Plants (MPIMP) database. 325-327 - Graham Dellaire, R. Farrall, Wendy A. Bickmore:
The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome. 328-330 - Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, Gert Vriend:
NRMD: Nuclear Receptor Mutation Database. 331-333 - Paul D. Thomas, Anish Kejariwal, Michael J. Campbell, Huaiyu Mi, Karen Diemer, Nan Guo, Istvan Ladunga, Betty Lazareva-Ulitsky, Anushya Muruganujan, Steven Rabkin, Jody A. Vandergriff, Olivier Doremieux:
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. 334-341 - Jason H. Tchieu, Fariba Fana, J. Lynn Fink, Jeffrey Harper, T. Murlidharan Nair, R. Hannes Niedner, Douglas W. Smith, Kenneth Steube, Tobey M. Tam, Stella Veretnik, Degeng Wang, Michael Gribskov:
The PlantsP and PlantsT Functional Genomics Databases. 342-344 - Cathy H. Wu, Lai-Su L. Yeh, Hongzhan Huang, Leslie Arminski, Jorge Castro-Alvear, Yongxing Chen, Zhang-Zhi Hu, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Cholanayakanahalli R. Vinayaka, Jian Zhang, Winona C. Barker:
The Protein Information Resource. 345-347 - Ori Sasson, Avishay Vaaknin, Hillel Fleischer, Elon Portugaly, Yonatan Bilu, Nathan Linial, Michal Linial:
ProtoNet: hierarchical classification of the protein space. 348-352 - Julien Grassot, Guy Mouchiroud, Guy Perrière:
RTKdb: database of receptor tyrosine kinase. 353-358 - Ovidiu Ivanciuc, Catherine H. Schein, Werner Braun:
SDAP: database and computational tools for allergenic proteins. 359-362 - Magnus Alm Rosenblad, Jan Gorodkin, Bjarne Knudsen, Christian Zwieb, Tore Samuelsson:
SRPDB: Signal Recognition Particle Database. 363-364 - Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-Claude Blatter, Anne Estreicher, Elisabeth Gasteiger, Maria Jesus Martin, Karine Michoud, Claire O'Donovan, Isabelle Phan, Sandrine Pilbout, Michel Schneider:
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. 365-370 - Daniel H. Haft, Jeremy D. Selengut, Owen White:
The TIGRFAMs database of protein families. 371-373 - V. Matys, Ellen Fricke, R. Geffers, Ellen Gößling, Martin Haubrock, Reinhard Hehl, Klaus Hornischer, Dagmar Karas, Alexander E. Kel, Olga V. Kel-Margoulis, Dorothee-U. Kloos, Sigrid Land, Birgit Lewicki-Potapov, Holger Michael, Richard Münch, Ingmar Reuter, Stella Rotert, H. Saxel, Maurice Scheer, S. Thiele, Edgar Wingender:
TRANSFAC®: transcriptional regulation, from patterns to profiles. 374-378 - Angelo M. Facchiano, Antonio Facchiano, Francesco Facchiano:
Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences. 379-382 - Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Anna R. Panchenko, Bachoti S. Rao, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant:
CDD: a curated Entrez database of conserved domain alignments. 383-387 - Evgenia V. Kriventseva, Florence Servant, Rolf Apweiler:
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters. 388-389 - Hongzhan Huang, Winona C. Barker, Yongxing Chen, Cathy H. Wu:
iProClass: an integrated database of protein family, function and structure information. 390-392 - Tanja la Cour, Ramneek Gupta, Kristoffer Rapacki, Karen Skriver, Flemming M. Poulsen, Søren Brunak:
NESbase version 1.0: a database of nuclear export signals. 393-396 - Rajesh Nair, Phil Carter, Burkhard Rost:
NLSdb: database of nuclear localization signals. 397-399 - Terri K. Attwood, Paul Bradley, Darren R. Flower, Anna Gaulton, Neil Maudling, Alex L. Mitchell, G. Moulton, A. Nordle, K. Paine, P. Taylor, A. Uddin, Christianna Zygouri:
PRINTS and its automatic supplement, prePRINTS. 400-402 - Kristian Vlahovicek, László Kaján, János Murvai, Zoltán Hegeds, Sándor Pongor:
The SBASE domain sequence library, release 10: domain architecture prediction. 403-405 - Masami Ikeda, Masafumi Arai, Toshikatsu Okuno, Toshio Shimizu:
TMPDB: a database of experimentally-characterized transmembrane topologies. 406-409 - Phil Carter, Jinfeng Liu, Burkhard Rost:
PEP: Predictions for Entire Proteomes. 410-413 - Manuela Pruess, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul J. Kersey, Evgenia V. Kriventseva, Virginie Mittard, Nicola J. Mulder, Isabelle Phan, Florence Servant, Rolf Apweiler:
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. 414-417 - Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis:
REBASE: restriction enzymes and methyltransferases. 418-420 - Tala Bakheet, Bryan R. G. Williams, Khalid S. A. Khabar:
ARED 2.0: an update of AU-rich element mRNA database. 421-423 - Lixin Dai, Navtej Toor, Robert Olson, Andrew Keeping, Steven Zimmerly:
Database for mobile group II introns. 424-426 - Sophie Bonnal, Christel Boutonnet, Leonel Prado-Lourenço, Stéphan Vagner:
IRESdb: the Internal Ribosome Entry Site database. 427-428 - Maciej Szymanski, Volker A. Erdmann, Jan Barciszewski:
Noncoding regulatory RNAs database. 429-431 - John W. S. Brown, Manuel Echeverria, Liang-Hu Qu, Todd M. Lowe, Jean-Pierre Bachellerie, Alexander Hüttenhofer, James P. Kastenmayer, Pamela J. Green, Paul D. Shaw, David F. Marshall:
Plant snoRNA database. 432-435 - Guglielmo Rainaldi, Mariateresa Volpicella, Flavio Licciulli, Sabino Liuni, Raffaele Gallerani, Luigi R. Ceci:
PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes. 436-438 - Sam Griffiths-Jones, Alex Bateman, Mhairi Marshall, Ajay Khanna, Sean R. Eddy:
Rfam: an RNA family database. 439-441 - James R. Cole, Benli Chai, Terry L. Marsh, Ryan J. Farris, Qiong Wang, S. A. Kulam, S. Chandra, Donna M. McGarrell, Thomas M. Schmidt, George M. Garrity, James M. Tiedje:
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. 442-443 - Martin Pelchat, Lynda Rocheleau, Jonathan Perreault, Jean-Pierre Perreault:
SubViral RNA: a database of the smallest known auto-replicable RNA species. 444-445 - Christian Zwieb, Jan Gorodkin, Bjarne Knudsen, Jody Burks, Jacek Wower:
tmRDB (tmRNA database). 446-447 - S. S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi, Krishna Sekar:
CADB: Conformation Angles DataBase of proteins. 448-451 - Frances M. G. Pearl, C. F. Bennett, James E. Bray, Andrew P. Harrison, Nigel J. Martin, Adrian J. Shepherd, Ian Sillitoe, Janet M. Thornton, Christine A. Orengo:
The CATH database: an extended protein family resource for structural and functional genomics. 452-455 - Giacomo Finocchiaro, Ting Wang, René Hoffmann, Aitor González, Rebecca C. Wade:
DSMM: a Database of Simulated Molecular Motions. 456-457 - Harry Boutselakis, Dimitris Dimitropoulos, Joël Fillon, Adel Golovin, Kim Henrick, A. Hussain, John M. C. Ionides, Melford John, Peter A. Keller, Evgeny B. Krissinel, P. McNeil, Avi Naim, Richard H. Newman, Thomas J. Oldfield, Jorge Pineda, Abdel-Krim Rachedi, J. Copeland, Andrey Sitnov, Siamak Sobhany, Antonio Suarez-Uruena, Jawahar Swaminathan, Mohammed Tagari, John G. Tate, Swen Tromm, Samir S. Velankar, Wim F. Vranken:
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. 458-462 - Akihiro Yamaguchi, Mitsuo Iwadate, Ei-Ichiro Suzuki, Kei Yura, Shigetsugu Kawakita, Hideaki Umeyama, Mitiko Go:
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species. 463-468 - Daniel W. A. Buchan, Stuart C. G. Rison, James E. Bray, David A. Lee, Frances M. G. Pearl, Janet M. Thornton, Christine A. Orengo:
Gene3D: structural assignments for the biologist and bioinformaticist alike. 469-473 - Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant:
MMDB: Entrez's 3D-structure database. 474-477 - Nathaniel Echols, Duncan Milburn, Mark Gerstein:
MolMovDB: analysis and visualization of conformational change and structural flexibility. 478-482 - Wing Lok Abe Kurtz Chiu, Chun Ngai Sze, Nap Tak Ma, Lai Fan Chiu, Chung Wai Leung, Steve Chik Fun Au-Yeung:
NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0. 483-485 - V. S. Gowri, Shashi B. Pandit, P. S. Karthik, Narayanaswamy Srinivasan, S. Balaji:
Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. 486-488 - John D. Westbrook, Zukang Feng, Li Chen, Huanwang Yang, Helen M. Berman:
The Protein Data Bank and structural genomics. 489-491 - Tamotsu Noguchi, Yutaka Akiyama:
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003. 492-493 - Andrea Schafferhans, Joachim E. W. Meyer, Seán I. O'Donoghue:
The PSSH database of alignments between protein sequences and tertiary structures. 494-498 - John S. Garavelli:
The RESID Database of Protein Modifications: 2003 developments. 499-501 - Venkatesh L. Murthy, George D. Rose:
RNABase: an annotated database of RNA structures. 502-504 - Ranyee A. Chiang, Elaine C. Meng, Conrad C. Huang, Thomas E. Ferrin, Patricia C. Babbitt:
The Structure Superposition Database. 505-510 - Catherine A. Cooper, Hiren J. Joshi, Mathew J. Harrison, Marc R. Wilkins, Nicolle H. Packer:
GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003, update. 511-513 - Alexander Loy, Matthias Horn, Michael Wagner:
probeBase: an online resource for rRNA-targeted oligonucleotide probes. 514-516
Volume 31, Number 13, July 2003
- Krzysztof Ginalski, Leszek Rychlewski:
Detection of reliable and unexpected protein fold predictions using 3D-Jury. 3291-3292 - Phil Carter, Claus A. F. Andersen, Burkhard Rost:
DSSPcont: continuous secondary structure assignments for proteins. 3293-3295 - Ling-Hong Hung, Ram Samudrala:
PROTINFO: secondary and tertiary protein structure prediction. 3296-3299 - Burkhard Rost, Jinfeng Liu:
The PredictProtein server. 3300-3304 - Michal A. Kurowski, Janusz M. Bujnicki:
GeneSilico protein structure prediction meta-server. 3305-3307 - Volker A. Eyrich, Burkhard Rost:
META-PP: single interface to crucial prediction servers. 3308-3310 - Ingrid Y. Y. Koh, Volker A. Eyrich, Marc A. Martí-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, Narayanan Eswar, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Andrej Sali, Burkhard Rost:
EVA: evaluation of protein structure prediction servers. 3311-3315 - Leigh Willard, Anuj Ranjan, Haiyan Zhang, Hassan Monzavi, Robert F. Boyko, Brian D. Sykes, David S. Wishart:
VADAR: a web server for quantitative evaluation of protein structure quality. 3316-3319 - Patrice Gouet, Xavier Robert, Emmanuel Courcelle:
ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. 3320-3323 - Mike P. Liang, D. Rey Banatao, Teri E. Klein, Douglas L. Brutlag, Russ B. Altman:
WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures. 3324-3327 - Steven P. Bennett, Lin Lu, Douglas L. Brutlag:
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs. 3328-3332 - Anna Gaulton, Terri K. Attwood:
Motif3D: relating protein sequence motifs to 3D structure. 3333-3336 - Rajesh Nair, Burkhard Rost:
LOC3D: annotate sub-cellular localization for protein structures. 3337-3340 - Alexander Stark, Robert B. Russell:
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. 3341-3344 - M. Madan Babu:
NCI: a server to identify non-canonical interactions in protein structures. 3345-3348 - Razif R. Gabdoulline, Rebecca C. Wade, Dirk Walther:
MolSurfer: a macromolecular interface navigator. 3349-3351 - T. Andrew Binkowski, Shapor Naghibzadeh, Jie Liang:
CASTp: Computed Atlas of Surface Topography of proteins. 3352-3355 - A. S. Z. Hussain, Ch. Kiran Kumar, C. K. Rajesh, S. S. Sheik, Krishna Sekar:
SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules. 3356-3358 - Zsuzsanna Dosztányi, Csaba Magyar, Gábor E. Tusnády, Miklós Cserzo, András Fiser, István Simon:
Servers for sequence-structure relationship analysis and prediction. 3359-3363 - Luigi Cavallo, Jens Kleinjung, Franca Fraternali:
POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level. 3364-3366 - Takeshi Kawabata:
MATRAS: a program for protein 3D structure comparison. 3367-3369 - Adam T. Zemla:
LGA: a method for finding 3D similarities in protein structures. 3370-3374 - Narayanan Eswar, Bino John, Nebojsa Mirkovic, András Fiser, Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Martí-Renom, Mallur S. Madhusudhan, Bozidar Yerkovich, Andrej Sali:
Tools for comparative protein structure modeling and analysis. 3375-3380 - Torsten Schwede, Jürgen Kopp, Nicolas Guex, Manuel C. Peitsch:
SWISS-MODEL: an automated protein homology-modeling server. 3381-3385 - Goran Neshich, Roberto C. Togawa, Adauto L. Mancini, Paula R. Kuser, Michel E. B. Yamagishi, Georgios Joannis Pappas Jr., Wellington V. Torres, Tharsis Fonseca e Campos, Leonardo L. Ferreira, Fabio M. Luna, Adilton G. Oliveira, Ronald T. Miura, Marcus K. Inoue, Luiz G. Horita, Dimas F. de Souza, Fabiana Dominiquini, Alexandre Alvaro, Cleber S. Lima, Fabio O. Ogawa, Gabriel B. Gomes, Juliana F. Palandrani, Gabriela F. dos Santos, Esther M. de Freitas, Amanda R. Mattiuz, Ivan C. Costa, Celso L. de Almeida, Savio Souza, Christian Baudet, Roberto H. Higa:
STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence. 3386-3392 - Guy Perrière, Christophe Combet, Simon Penel, Christophe Blanchet, Jean Thioulouse, Christophe Geourjon, Julien Grassot, Céline Charavay, Manolo Gouy, Laurent Duret, Gilbert Deléage:
Integrated databanks access and sequence/structure analysis services at the PBIL. 3393-3399 - Emmanuel Bettler, Roland Krause, Florence Horn, Gert Vriend:
NRSAS: Nuclear Receptor Structure Analysis Servers. 3400-3403 - V. Shanthi, P. Selvarani, Ch. Kiran Kumar, C. S. Mohire, Krishna Sekar:
SSEP: secondary structural elements of proteins. 3404-3405 - Michael Zuker:
Mfold web server for nucleic acid folding and hybridization prediction. 3406-3415 - Mirela Andronescu, Rosalía Aguirre-Hernández, Anne Condon, Holger H. Hoos:
RNAsoft: a suite of RNA secondary structure prediction and design software tools. 3416-3422 - Bjarne Knudsen, Jotun Hein:
Pfold: RNA secondary structure prediction using stochastic context-free grammars. 3423-3428 - Ivo L. Hofacker:
Vienna RNA secondary structure server. 3429-3431 - Kyungsook Han, Yanga Byun:
PSEUDOVIEWER2: visualization of RNA pseudoknots of any type. 3432-3440 - Peter Bengert, Thomas Dandekar:
A software tool-box for analysis of regulatory RNA elements. 3441-3445 - Yuh-Jyh Hu:
GPRM: a genetic programming approach to finding common RNA secondary structure elements. 3446-3449 - Huanwang Yang, Fabrice Jossinet, Neocles Leontis, Li Chen, John D. Westbrook, Helen M. Berman, Eric Westhof:
Tools for the automatic identification and classification of RNA base pairs. 3450-3460 - Javier Herrero, Fátima Al-Shahrour, Ramón Díaz-Uriarte, Álvaro Mateos, Juan M. Vaquerizas, Javier Santoyo, Joaquín Dopazo:
GEPAS: a web-based resource for microarray gene expression data analysis. 3461-3467 - Bert Coessens, Gert Thijs, Stein Aerts, Kathleen Marchal, Frank De Smet, Kristof Engelen, Patrick Glenisson, Yves Moreau, Janick Mathys, Bart De Moor:
INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis. 3468-3470 - Steen Knudsen, Christopher T. Workman, Thomas Sicheritz-Pontén, Carsten Friis:
GenePublisher: automated analysis of DNA microarray data. 3471-3476 - Nicholas M. Luscombe, Thomas E. Royce, Paul Bertone, Nathaniel Echols, Christine E. Horak, Joseph T. Chang, Michael Snyder, Mark Gerstein:
ExpressYourself: a modular platform for processing and visualizing microarray data. 3477-3482 - Sheng Zhong, Cheng Li, Wing Hung Wong:
ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis. 3483-3486 - Crispin Roven, Harmen J. Bussemaker:
REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data. 3487-3490 - Henrik Bjørn Nielsen, Rasmus Wernersson, Steen Knudsen:
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays. 3491-3496 - Chenna Ramu, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie Dawn Thompson:
Multiple sequence alignment with the Clustal series of programs. 3497-3500 - Davinder K. Kohli, Anand K. Bachhawat:
CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics. 3501-3502 - Olivier Poirot, Eamonn O'Toole, Cédric Notredame:
Tcoffee add igs: a web server for computing, evaluating and combining multiple sequence alignments. 3503-3506 - Simon Cawley, Lior Pachter, Marina Alexandersson:
SLAM web server for comparative gene finding and alignment. 3507-3509 - Yvonne J. K. Edwards, Tim J. Carver, Tanya Vavouri, Martin C. Frith, Martin J. Bishop, Greg Elgar:
Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence. 3510-3517 - Scott Schwartz, Laura Elnitski, Mei Li, Matthew T. Weirauch, Cathy Riemer, Arian Smit, Eric D. Green, Ross C. Hardison, Webb Miller:
MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. 3518-3524 - Nicolas Bray, Lior Pachter:
MAVID multiple alignment server. 3525-3526 - Liliana Florea, Michael McClelland, Cathy Riemer, Scott Schwartz, Webb Miller:
EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae. 3527-3532 - Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan:
MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences. 3533-3536 - Rasmus Wernersson, Anders Gorm Pedersen:
RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. 3537-3539 - Victor V. Solovyev, Ilham A. Shahmuradov:
PromH: promoters identification using orthologous genomic sequences. 3540-3545 - Allen Chong, Guanglan Zhang, Vladimir B. Bajic:
FIE2: a program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes. 3546-3553 - Anason S. Halees, Dmitriy Leyfer, Zhiping Weng:
PromoSer: a large-scale mammalian promoter and transcription start site identification service. 3554-3559 - Vladimir B. Bajic, Seng Hong Seah:
Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes. 3560-3563 - Anton Nekrutenko, Wen-Yu Chung, Wen-Hsiung Li:
ETOPE: evolutionary test of predicted exons. 3564-3567 - Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang, Adrian R. Krainer:
ESEfinder: a web resource to identify exonic splicing enhancers. 3568-3571 - Paul E. Boardman, Stephen G. Oliver, Simon J. Hubbard:
SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences. 3572-3575 - Alexander E. Kel, Ellen Gößling, Ingmar Reuter, Evgeny Cheremushkin, Olga V. Kel-Margoulis, Edgar Wingender:
MATCHTM: a tool for searching transcription factor binding sites in DNA sequences. 3576-3579 - William A. Thompson, Eric C. Rouchka, Charles E. Lawrence:
Gibbs Recursive Sampler: finding transcription factor binding sites. 3580-3585 - Saurabh Sinha, Martin Tompa:
YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation. 3586-3588 - Alona Sosinsky, Christopher P. Bonin, Richard S. Mann, Barry Honig:
Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors. 3589-3592 - Jacques van Helden:
Regulatory Sequence Analysis Tools. 3593-3596 - Shannon D. Schlueter, Qunfeng Dong, Volker Brendel:
GeneSeqer add PlantGDB: gene structure prediction in plant genomes. 3597-3600 - William H. Majoros, Mihaela Pertea, Corina Antonescu, Steven Salzberg:
GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders. 3601-3604 - Vladimir B. Bajic, Sin Lam Tan, Allen Chong, Suisheng Tang, Anders Ström, Jan-Åke Gustafsson, Chin-Yo Lin, Edison T. Liu:
Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes. 3605-3607 - Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà, Graziano Pesole:
PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences. 3608-3612 - Jennifer L. Gardy, Cory Spencer, Ke Wang, Martin Ester, Gábor E. Tusnády, István Simon, Sujun Hua, Katalin de Fays, Christophe G. Lambert, Kenta Nakai, Fiona S. L. Brinkman:
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria. 3613-3617 - Giovanna Ambrosini, Viviane Praz, Vidhya Jagannathan, Philipp Bucher:
Signal search analysis server. 3618-3620 - Pingping Guan, Irini A. Doytchinova, Christianna Zygouri, Darren R. Flower:
MHCPred: a server for quantitative prediction of peptide-MHC binding. 3621-3624 - Pål Puntervoll, Rune Linding, Christine Gemünd, Sophie Chabanis-Davidson, Morten Mattingsdal, Scott Cameron, David M. A. Martin, Gabriele Ausiello, Barbara Brannetti, Anna Costantini, Fabrizio Ferrè, Vincenza Maselli, Allegra Via, Gianni Cesareni, Francesca Diella, Giulio Superti-Furga, Lucjan Stanislaw Wyrwicz, Chenna Ramu, Caroline McGuigan, Rambabu Gudavalli, Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N. Hunter, Rein Aasland, Toby J. Gibson:
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. 3625-3630 - Frank Eisenhaber, Birgit Eisenhaber, Werner Kubina, Sebastian Maurer-Stroh, Georg Neuberger, Georg Schneider, Michael Wildpaner:
Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-, NMT and PTS1. 3631-3634 - John C. Obenauer, Lewis C. Cantley, Michael B. Yaffe:
Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs. 3635-3641 - Andrew Kernytsky, Burkhard Rost:
Static benchmarking of membrane helix predictions. 3642-3644 - Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel E. Platt, Tetsuo Shibuya:
The web server of IBM's Bioinformatics and Pattern Discovery group. 3645-3650 - Domènec Farré, Roman Roset, Mario Huerta, José-Enrique Adsuara, Llorenç Roselló, M. Mar Albà, Xavier Messeguer:
Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. 3651-3653 - Gitanjali Yadav, Rajesh S. Gokhale, Debasisa Mohanty:
SEARCHPKS: a program for detection and analysis of polyketide synthase domains. 3654-3658 - Guojun Yang, Timothy C. Hall:
MAK, a computational tool kit for automated MITE analysis. 3659-3665 - Martin C. Frith, Michael C. Li, Zhiping Weng:
Cluster-Buster: finding dense clusters of motifs in DNA sequences. 3666-3668 - David Robelin, Hugues Richard, Bernard Prum:
SIC: a tool to detect short inverted segments in a biological sequence. 3669-3671 - Roman M. Kolpakov, Ghizlane Bana, Gregory Kucherov:
mreps: efficient and flexible detection of tandem repeats in DNA. 3672-3678 - Hugues Richard, Grégory Nuel:
SPA: simple web tool to assess statistical significance of DNA patterns. 3679-3681 - Moshe Gal, Tzvi Katz, Amir Ovadia, Gad Yagil:
TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts. 3682-3685 - Kristian Vlahovicek, László Kaján, Sándor Pongor:
DNA analysis servers: plot.it, bend.it, model.it and IS. 3686-3687 - Tamas Vincze, Janos Posfai, Richard J. Roberts:
NEBcutter: a program to cleave DNA with restriction enzymes. 3688-3691 - Congzhong Cai, L. Y. Han, Zhi Liang Ji, X. Chen, Yu Zong Chen:
SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence. 3692-3697 - Paul D. Taylor, Terri K. Attwood, Darren R. Flower:
BPROMPT: a consensus server for membrane protein prediction. 3698-3700 - Rune Linding, Robert B. Russell, Victor Neduva, Toby J. Gibson:
GlobPlot: exploring protein sequences for globularity and disorder. 3701-3708 - Barbara Brannetti, Manuela Helmer-Citterich:
iSPOT: a web tool to infer the interaction specificity of families of protein modules. 3709-3711 - Steffen Hennig, Detlef Groth, Hans Lehrach:
Automated Gene Ontology annotation for anonymous sequence data. 3712-3715 - Agnes Hotz-Wagenblatt, Thomas Hankeln, Peter Ernst, Karl-Heinz Glatting, Erwin R. Schmidt, Sándor Suhai:
ESTAnnotator: a tool for high throughput EST annotation. 3716-3719 - François Enault, Karsten Suhre, Olivier Poirot, Chantal Abergel, Jean-Michel Claverie:
Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes. 3720-3722 - Stéphanie Bocs, Stéphane Cruveiller, David Vallenet, Grégory Nuel, Claudine Médigue:
AMIGene: Annotation of MIcrobial Genes. 3723-3726 - Hideaki Sugawara, Satoru Miyazaki:
AHMII: Agent to Help Microbial Information Integration. 3727-3728 - Chunyu Liu, Tom I. Bonner, Tu H. Nguyen, Jennifer L. Lyons, Susan L. Christian, Elliot S. Gershon:
DNannotator: annotation software tool kit for regional genomic sequences. 3729-3735 - Jason E. McDermott, Ram Samudrala:
Bioverse: functional, structural and contextual annotation of proteins and proteomes. 3736-3737 - Thomas Schiex, Jérôme Gouzy, Annick Moisan, Yannick de Oliveira:
FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. 3738-3741 - Sylvain Foissac, Philippe Bardou, Annick Moisan, Marie-Josée Cros, Thomas Schiex:
EUGÈNE'HOM: a generic similarity-based gene finder using multiple homologous sequences. 3742-3745 - Scott J. Emrich, Mary Lowe, Arthur L. Delcher:
PROBEmer: a web-based software tool for selecting optimal DNA oligos. 3746-3750 - S. H. Chen, C. Y. Lin, C. S. Cho, C. Z. Lo, C. A. Hsiung:
Primer Design Assistant (PDA): a web-based primer design tool. 3751-3754 - Guoqing Lu, Michael T. Hallett, Stephanie Pollock, David Y. Thomas:
DePIE: Designing Primers for Protein Interaction Experiments. 3755-3757 - Niels Tolstrup, Peter S. Nielsen, Jens G. Kolberg, Annett M. Frankel, Henrik Vissing, Sakari Kauppinen:
OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. 3758-3762 - Timothy Rose, Jorja G. Henikoff, Steven Henikoff:
CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. 3763-3766 - Alexander Sczyrba, Jan Krüger, Henning Mersch, Stefan Kurtz, Robert Giegerich:
RNA-related tools on the Bielefeld Bioinformatics Server. 3767-3770 - Chenna Ramu:
SIRW: a web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches. 3771-3774 - Sorin Draghici, Purvesh Khatri, Pratik Bhavsar, Abhik Shah, Stephen A. Krawetz, Michael A. Tainsky:
Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. 3775-3781 - Laurent Falquet, Lorenza Bordoli, Vassilios Ioannidis, Marco Pagni, C. Victor Jongeneel:
Swiss EMBnet node web server. 3782-3783 - Elisabeth Gasteiger, Alexandre Gattiker, Christine Hoogland, Ivan Ivanyi, Ron D. Appel, Amos Bairoch:
ExPASy: the proteomics server for in-depth protein knowledge and analysis. 3784-3788 - Sven Mika, Burkhard Rost:
UniqueProt: creating representative protein sequence sets. 3789-3791 - Konstantinos Bimpikis, Aidan Budd, Rune Linding, Toby J. Gibson:
BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases. 3792-3794 - Rodrigo Lopez, Ville Silventoinen, Stephen Robinson, Asif Kibria, Warren Gish:
WU-Blast2 server at the European Bioinformatics Institute. 3795-3798 - Günther Zehetner:
OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms. 3799-3803 - Krzysztof Ginalski, Jakub Pas, Lucjan Stanislaw Wyrwicz, Marcin von Grotthuss, Janusz M. Bujnicki, Leszek Rychlewski:
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure. 3804-3807 - Nicholas E. Taylor, Elizabeth A. Greene:
PARSESNP: a tool for the analysis of nucleotide polymorphisms. 3808-3811 - Pauline C. Ng, Steven Henikoff:
SIFT: predicting amino acid changes that affect protein function. 3812-3814 - Guillaume Albini, Matthieu Falque, Johann Joets:
ActionMap: a web-based software that automates loci assignments to framework maps. 3815-3818 - Yanlin Huang, David Kowalski:
WEB-THERMODYN: sequence analysis software for profiling DNA helical stability. 3819-3821 - I. Q. H. Phan, Sandrine Pilbout, Wolfgang Fleischmann, Amos Bairoch:
NEWT, a new taxonomy portal. 3822-3823 - Michal Lapidot, Yitzhak Pilpel:
Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. 3824-3828 - Frédéric Plewniak, Laurent Bianchetti, Yann Brelivet, Annaick Carles, Frédéric Chalmel, Odile Lecompte, Thiebaut Mochel, Luc Moulinier, Arnaud Muller, Jean Muller, Veronique Prigent, Raymond Ripp, Jean-Claude Thierry, Julie Dawn Thompson, Nicolas Wicker, Olivier Poch:
PipeAlign: a new toolkit for protein family analysis. 3829-3832 - Jinfeng Liu, Burkhard Rost:
NORSp: predictions of long regions without regular secondary structure. 3833-3835 - Hideaki Sugawara, Satoru Miyazaki:
Biological SOAP servers and web services provided by the public sequence data bank. 3836-3839 - Mathieu Blanchette, Martin Tompa:
FootPrinter: a program designed for phylogenetic footprinting. 3840-3842 - Edouard Yeramian, Louis M. Jones:
GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives. 3843-3849 - Niko Beerenwinkel, Martin Däumer, Mark Oette, Klaus Korn, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, Joachim Selbig, Hauke Walter:
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes. 3850-3855 - Lucy Skrabanek, Fabien Campagne, Harel Weinstein:
Building protein diagrams on the web with the residue-based diagram editor RbDe. 3856-3858 - Aaron J. Mackey, Timothy A. J. Haystead, William R. Pearson:
CRP: Cleavage of Radiolabeled Phosphoproteins. 3859-3861 - Karsten Hiller, Max Schobert, Claudia Hundertmark, Dieter Jahn, Richard Münch:
JVirGel: calculation of virtual two-dimensional protein gels. 3862-3865 - Carolina Perez-Iratxeta, Antonio J. Pérez-Pulido, Peer Bork, Miguel A. Andrade:
Update on XplorMed: a web server for exploring scientific literature. 3866-3868
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