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Nucleic 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
GenBank: update. 23-26 - Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane
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
atabase resources of the National Center for Biotechnology Information: update. 35-40 - Hans-Werner Mewes, Clara Amid
MIPS: analysis and annotation of proteins from whole genomes. 41-44 - Raphaël Leplae, Aline Hebrant, Shoshana J. Wodak
ACLAME: A CLAssification of Mobile genetic Elements. 45-49 - Jan 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
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
HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. 86-90 - Albin Sandelin
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
PIRSF: family classification system at the Protein Information Resource. 112-114 - Rolf Apweiler
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
Recent improvements to the PROSITE database. 134-137 - Alex Bateman
The Pfam protein families database. 138-141 - Ivica Letunic
SMART 4.0: towards genomic data integration. 142-144 - Thierry Hotelier, Ludovic Renault
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
The KNOTTIN website and database: a new information system dedicated to the knottin scaffold. 156-159 - Neil D. Rawlings
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
RPG: the Ribosomal Protein Gene database. 168-170 - Antonio Hermoso
TrSDB: a proteome database of transcription factors. 171-173 - Michael M. Hoffman
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
ArchDB: automated protein loop classification as a tool for structural genomics. 185-188 - John-Marc Chandonia
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
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
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
E-MSD: an integrated data resource for bioinformatics. 211-216 - Ursula Pieper
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
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
The SUPERFAMILY database in 2004: additions and improvements. 235-239 - Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni
SURFACE: a database of protein surface regions for functional annotation. 240-244 - Keiran Fleming, Arne Müller, Robert M. MacCallum
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
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
FusionDB: a database for in-depth analysis of prokaryotic gene fusion events. 273-276 - Minoru Kanehisa, Susumu Goto, Shuichi Kawashima
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
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
coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. 296-299 - Margrethe H. Serres
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
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
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
Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. 315-318 - Taro L. Saito, Miwaka Ohtani, Hiroshi Sawai, Fumi Sano, Ayaka Saka, Daisuke Watanabe
SCMD: Saccharomyces cerevisiae Morphological Database. 319-322 - Gaëlle Lelandais, Stéphane Le Crom
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
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
GeneDB: a resource for prokaryotic and eukaryotic organisms. 339-343 - Michael Luchtan
TcruziDB: an integrated Trypanosoma cruzi genome resource. 344-346 - Franck Samson, Véronique Brunaud, Sylvain Duchêne, Yannick de Oliveira
FLAGdb++: a database for the functional analysis of the Arabidopsis genome. 347-350 - S. Mohseni-Zadeh, Alexandra Louis
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
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
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
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
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
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
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
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. 423-426 - John Parkinson, Claire Whitton, Ralf Schmid
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
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
The aMAZE LightBench: a web interface to a relational database of cellular processes. 443-448 - Lukasz Salwínski
The Database of Interacting Proteins: 2004 update. 449-451 - Henning Hermjakob
IntAct: an open source molecular interaction database. 452-455 - Ming Chen
STCDB: Signal Transduction Classification Database. 456-458 - Christophe Andreoli, Holger Prokisch
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
Ensembl 2004. 468-470 - Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky
FREP: a database of functional repeats in mouse cDNAs. 471-475 - Carol J. Bult, Judith A. Blake
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
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
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
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
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
Pathbase: a database of mutant mouse pathology. 512-515 - D. Fredman, G. Munns, Daniel Rios, F. Sjöholm, Marianne Siegfried, Boris Lenhard
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
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
EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. 548-551 - Axel Visel
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
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
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
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
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
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
CVTree: a phylogenetic tree reconstruction tool based on whole genomes. 45-47 - Radek Zika, Jan 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
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
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
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
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
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
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
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
CARNAC: folding families of related RNAs. 142-145 - Jianhua Ruan
ILM: a web server for predicting RNA secondary structures with pseudoknots. 146-149 - Xiaomin Ying, Hong Luo
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
The ERPIN server: an interface to profile-based RNA motif identification. 160-165 - Sònia Casillas
PDA: a pipeline to explore and estimate polymorphism in large DNA databases. 166-169 - Stefan Weckx, Peter De Rijk
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
Gene2Oligo: oligonucleotide design for in vitro gene synthesis. 176-180 - Namshin Kim
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences. 181-186 - William G. Fairbrother
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. 187-190 - Anason S. Halees
PromoSer: improvements to the algorithm, visualization and accessibility. 191-194 - Wynand Alkema
MSCAN: identification of functional clusters of transcription factor binding sites. 195-198 - Giulio Pavesi
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
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
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. 213-216 - Gabriela G. Loots
rVISTA 2.0: evolutionary analysis of transcription factor binding sites. 217-221 - Matti Kankainen
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
Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining. 230-234 - Zhenjun Hu, Yutao Fu, Anason S. Halees
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. 235-241 - Lucía Conde
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. 242-248 - Albin Sandelin
ConSite: web-based prediction of regulatory elements using cross-species comparison. 249-252 - Roded Sharan, Asa Ben-Hur, Gabriela G. Loots
CREME: Cis-Regulatory Module Explorer for the human genome. 253-256 - Vinsensius B. Vega, Dhinoth Kumar Bangarusamy
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
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. 267-272 - Kelly A. Frazer
VISTA: computational tools for comparative genomics. 273-279 - Ivan Ovcharenko, Marcelo A. Nobrega, Gabriela G. Loots
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. 280-286 - José L. Oliver
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
e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences. 301-304 - Leila Taher
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
The PredictProtein server. 321-326 - Aron Marchler-Bauer
CD-Search: protein domain annotations on the fly. 327-331 - Marco Pagni
MyHits: a new interactive resource for protein annotation and domain identification. 332-335 - François Enault, Karsten Suhre
Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis. 336-339 - Richard D. LeDuc
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
CysView: protein classification based on cysteine pairing patterns. 350-355 - Lesheng Kong
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins. 356-359 - Brian D. O'Connor
GDAP: a web tool for genome-wide protein disulfide bond prediction. 360-364 - Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart
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
PrediSi: prediction of signal peptides and their cleavage positions. 375-379 - Panagiotis K. Papasaikas
PRED-GPCR: GPCR recognition and family classification server. 380-382 - Manoj Bhasin
GPCRpred: an SVM-based method for prediction of families and subfamilies of G-protein coupled receptors. 383-389 - Masafumi Arai, Hironori Mitsuke, Masami Ikeda
ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. 390-393 - Frode S. Berven, Kristian Flikka
BOMP: a program to predict integral ?barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. 394-399 - Pantelis G. Bagos
PRED-TMBB: a web server for predicting the topology of ?barrel outer membrane proteins. 400-404 - Mohd. Zeeshan Ansari, Gitanjali Yadav
NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. 405-413 - Manoj Bhasin
ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. 414-419 - Yutao Fu, Martin C. Frith
MotifViz: an analysis and visualization tool for motif discovery. 420-423 - Olga V. Kalinina
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
The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species. 429-434 - Véronique Giudicelli
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
ArrayProspector: a web resource of functional associations inferred from microarray expression data. 445-448 - Purvesh Khatri
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
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
Expression Profiler: next generation - an online platform for analysis of microarray data. 465-470 - Fiona M. Roche
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
New challenges in gene expression data analysis and the extended GEPAS. 485-491 - Stefano Volinia
GOAL: automated Gene Ontology analysis of expression profiles. 492-499 - Matthias Heinig
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
BioInfo3D: a suite of tools for structural bioinformatics. 503-507 - R. Gautier, Anne-Claude Camproux
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
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. 522-525 - David E. Kim
Protein structure prediction and analysis using the Robetta server. 526-531 - Andrew E. Torda, James B. Procter
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
SA-Search: a web tool for protein structure mining based on a Structural Alphabet. 545-548 - Vladimir A. Ivanisenko
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
JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. 595-601 - Anirban Bhaduri, Ganesan Pugalenthi
iMOT: an interactive package for the selection of spatially interacting motifs. 602-605 - Jean-Baptiste Claude
CaspR: a web server for automated molecular replacement using homology modelling. 606-609 - Karsten Suhre
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
CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison. 624-627 - Yuri L. Orlov
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
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
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
Isotopica: a tool for the calculation and viewing of complex isotopic envelopes. 674-678 - Zhi Wei Cao, Ying Xue
MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids. 679-685
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