| | Editorial Nucleic Acids Res. 2005 July 1; 33(Web Server issue): W1. Published online 2005 June 27. doi: 10.1093/nar/gki592.PMCID: PMC1160268 Articles The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers Joanne A. Fox, Stefanie L. Butland, Scott McMillan, Graeme Campbell, and B. F. Francis Ouellette PMCID: PMC1160270 SOAP-based services provided by the European Bioinformatics Institute S. Pillai, V. Silventoinen, K. Kallio, M. Senger, S. Sobhany, J. Tate, S. Velankar, A. Golovin, K. Henrick, P. Rice, P. Stoehr, and R. Lopez PMCID: PMC1160251 The Diamond STING server Goran Neshich, Luiz C. Borro, Roberto H. Higa, Paula R. Kuser, Michel E. B. Yamagishi, Eduardo H. Franco, Joao N. Krauchenco, Renato Fileto, André A. Ribeiro, George B. P. Bezerra, Thiago M. Velludo, Tomás S. Jimenez, Noboru Furukawa, Hirofumi Teshima, Koji Kitajima, Abdulla Bava, Akinori Sarai, Roberto C. Togawa, and Adauto L. Mancini PMCID: PMC1160158 Protein structure prediction servers at University College London Kevin Bryson, Liam J. McGuffin, Russell L. Marsden, Jonathan J. Ward, Jaspreet S. Sodhi, and David T. Jones PMCID: PMC1160171 SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment Vladimir Sobolev, Eran Eyal, Sergey Gerzon, Vladimir Potapov, Mariana Babor, Jaime Prilusky, and Marvin Edelman PMCID: PMC1160159 RPBS: a web resource for structural bioinformatics C. Alland, F. Moreews, D. Boens, M. Carpentier, S. Chiusa, M. Lonquety, N. Renault, Y. Wong, H. Cantalloube, J. Chomilier, J. Hochez, J. Pothier, B. O. Villoutreix, J.-F. Zagury, and P. Tufféry PMCID: PMC1160237 CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology Alessandro Paiardini, Francesco Bossa, and Stefano Pascarella PMCID: PMC1160177 Dcode.org anthology of comparative genomic tools Gabriela G. Loots and Ivan Ovcharenko PMCID: PMC1160116 PAT: a protein analysis toolkit for integrated biocomputing on the web Jérôme Gracy and Laurent Chiche PMCID: PMC1160216 SCRATCH: a protein structure and structural feature prediction server J. Cheng, A. Z. Randall, M. J. Sweredoski, and P. Baldi PMCID: PMC1160157 PROTINFO: new algorithms for enhanced protein structure predictions Ling-Hong Hung, Shing-Chung Ngan, Tianyun Liu, and Ram Samudrala PMCID: PMC1160164 ProTarget: automatic prediction of protein structure novelty Ori Sasson and Michal Linial PMCID: PMC1160150 Fragment Finder: a web-based software to identify similar three-dimensional structural motif P. Ananthalakshmi, Ch. Kiran Kumar, M. Jeyasimhan, K. Sumathi, and K. Sekar PMCID: PMC1160114 ProFunc: a server for predicting protein function from 3D structure Roman A. Laskowski, James D. Watson, and Janet M. Thornton PMCID: PMC1160175 PISCES: recent improvements to a PDB sequence culling server Guoli Wang and Roland L. Dunbrack, Jr PMCID: PMC1160163 WebProAnalyst: an interactive tool for analysis of quantitative structure–activity relationships in protein families Vladimir A. Ivanisenko, Alexey M. Eroshkin, and Nickolay A. Kolchanov PMCID: PMC1160182 LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST Dan Xie, Ao Li, Minghui Wang, Zhewen Fan, and Huanqing Feng PMCID: PMC1160120 AS2TS system for protein structure modeling and analysis A. Zemla, C. Ecale Zhou, T. Slezak, T. Kuczmarski, D. Rama, C. Torres, D. Sawicka, and D. Barsky PMCID: PMC1160218 InterProScan: protein domains identifier E. Quevillon, V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, and R. Lopez PMCID: PMC1160203 PhyloDome—visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets Maria Novatchkova, Michael Wildpaner, Dieter Schweizer, and Frank Eisenhaber PMCID: PMC1160134 PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families O. Krishnadev, N. Rekha, S. B. Pandit, S. Abhiman, S. Mohanty, L. S. Swapna, S. Gore, and N. Srinivasan PMCID: PMC1160235 DIAL: a web-based server for the automatic identification of structural domains in proteins Ganesan Pugalenthi, Govindaraju Archunan, and Ramanathan Sowdhamini PMCID: PMC1160188 pdbFun: mass selection and fast comparison of annotated PDB residues Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, and Manuela Helmer-Citterich PMCID: PMC1160259 PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands Pedro A. Reche and Ellis L. Reinherz PMCID: PMC1160118 GPCRsclass: a web tool for the classification of amine type of G-protein-coupled receptors Manoj Bhasin and G. P. S. Raghava PMCID: PMC1160112 GRIFFIN: a system for predicting GPCR–G-protein coupling selectivity using a support vector machine and a hidden Markov model Yukimitsu Yabuki, Takahiko Muramatsu, Takatsugu Hirokawa, Hidehito Mukai, and Makiko Suwa PMCID: PMC1160255 BhairPred: prediction of β-hairpins in a protein from multiple alignment information using ANN and SVM techniques Manish Kumar, Manoj Bhasin, Navjot K. Natt, and G. P. S. Raghava PMCID: PMC1160264 Scooby-domain: prediction of globular domains in protein sequence Richard A. George, Kuang Lin, and Jaap Heringa PMCID: PMC1160142 TMBETA-NET: discrimination and prediction of membrane spanning β-strands in outer membrane proteins M. Michael Gromiha, Shandar Ahmad, and Makiko Suwa PMCID: PMC1160128 CEP: a conformational epitope prediction server Urmila Kulkarni-Kale, Shriram Bhosle, and A. S. Kolaskar PMCID: PMC1160221 MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides Guang Lan Zhang, Asif M. Khan, Kellathur N. Srinivasan, J. Thomas August, and Vladimir Brusic PMCID: PMC1160213 PREDBALB/c: a system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse Guang Lan Zhang, Kellathur N. Srinivasan, Anitha Veeramani, J. Thomas August, and Vladimir Brusic PMCID: PMC1160239 GPS: a comprehensive www server for phosphorylation sites prediction Yu Xue, Fengfeng Zhou, Minjie Zhu, Kashif Ahmed, Guoliang Chen, and Xuebiao Yao PMCID: PMC1160154 TMB-Hunt: a web server to screen sequence sets for transmembrane β-barrel proteins Andrew G. Garrow, Alison Agnew, and David R. Westhead PMCID: PMC1160145 Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations Hongyi Zhou, Chi Zhang, Song Liu, and Yaoqi Zhou PMCID: PMC1160121 TRAMPLE: the transmembrane protein labelling environment Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, and Rita Casadio PMCID: PMC1160201 Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences Manoj Bhasin and G. P. S. Raghava PMCID: PMC1160263 GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences Christina Backes, Jan Kuentzer, Hans-Peter Lenhof, Nicole Comtesse, and Eckart Meese PMCID: PMC1160194 GlyProt: in silico glycosylation of proteins Andreas Bohne-Lang and Claus-Wilhelm von der Lieth PMCID: PMC1160146 SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites Pankaj Kamra, Rajesh S. Gokhale, and Debasisa Mohanty PMCID: PMC1160210 KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, and Jorng-Tzong Horng PMCID: PMC1160232 DiANNA: a web server for disulfide connectivity prediction F. Ferrè and P. Clote PMCID: PMC1160173 MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm Darby Tien-Hau Chang, Yen-Jen Oyang, and Jung-Hsin Lin PMCID: PMC1160262 REPPER—repeats and their periodicities in fibrous proteins Markus Gruber, Johannes Söding, and Andrei N. Lupas PMCID: PMC1160166 The HHpred interactive server for protein homology detection and structure prediction Johannes Söding, Andreas Biegert, and Andrei N. Lupas PMCID: PMC1160169 Fragnostic: walking through protein structure space Iddo Friedberg and Adam Godzik PMCID: PMC1160124 CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures Kristian Vlahoviček, Alessandro Pintar, Laavanya Parthasarathi, Oliviero Carugo, and Sándor Pongor PMCID: PMC1160123 QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns Roee Gutman, Carine Berezin, Roy Wollman, Yossi Rosenberg, and Nir Ben-Tal PMCID: PMC1160256 PatMatch: a program for finding patterns in peptide and nucleotide sequences Thomas Yan, Danny Yoo, Tanya Z. Berardini, Lukas A. Mueller, Dan C. Weems, Shuai Weng, J. Michael Cherry, and Seung Y. Rhee PMCID: PMC1160129 MINER: software for phylogenetic motif identification David La and Dennis R. Livesay PMCID: PMC1160226 SVC: structured visualization of evolutionary sequence conservation S. Roepcke, P. Fiziev, P. H. Seeburg, and M. Vingron PMCID: PMC1160265 SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs Saikat Chakrabarti, A. Prem Anand, Nitin Bhardwaj, Ganesan Pugalenthi, and R. Sowdhamini PMCID: PMC1160253 ProTeus: identifying signatures in protein termini Iris Bahir and Michal Linial PMCID: PMC1160132 One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries Milana Frenkel-Morgenstern, Alice Singer, Hagit Bronfeld, and Shmuel Pietrokovski PMCID: PMC1160248 FFAS03: a server for profile–profile sequence alignments Lukasz Jaroszewski, Leszek Rychlewski, Zhanwen Li, Weizhong Li, and Adam Godzik PMCID: PMC1160179 PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information V. A. Simossis and J. Heringa PMCID: PMC1160151 Manipulating multiple sequence alignments via MaM and WebMaM Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, and S. Cenk Sahinalp PMCID: PMC1160167 ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures Meytal Landau, Itay Mayrose, Yossi Rosenberg, Fabian Glaser, Eric Martz, Tal Pupko, and Nir Ben-Tal PMCID: PMC1160131 SRide: a server for identifying stabilizing residues in proteins Csaba Magyar, M. Michael Gromiha, Gerard Pujadas, Gábor E. Tusnády, and István Simon PMCID: PMC1160170 I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure Emidio Capriotti, Piero Fariselli, and Rita Casadio PMCID: PMC1160136 MutDB services: interactive structural analysis of mutation data Jessica Dantzer, Charles Moad, Randy Heiland, and Sean Mooney PMCID: PMC1160165 MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features William C. Ray PMCID: PMC1160135 PPG: online generation of protein pictures and animations Cédric Binisti, Ahmed Ali Salim, and Pierre Tufféry PMCID: PMC1160153 BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes Jason McDermott, Michal Guerquin, Zach Frazier, Aaron N. Chang, and Ram Samudrala PMCID: PMC1160162 Metabolic PathFinding: inferring relevant pathways in biochemical networks Didier Croes, Fabian Couche, Shoshana J. Wodak, and Jacques van Helden PMCID: PMC1160198 PRISM: protein interactions by structural matching Utkan Ogmen, Ozlem Keskin, A. Selim Aytuna, Ruth Nussinov, and Attila Gursoy PMCID: PMC1160261 SiteEngines: recognition and comparison of binding sites and protein–protein interfaces Alexandra Shulman-Peleg, Ruth Nussinov, and Haim J. Wolfson PMCID: PMC1160242 POPSCOMP: an automated interaction analysis of biomolecular complexes Jens Kleinjung and Franca Fraternali PMCID: PMC1160130 EVAcon: a protein contact prediction evaluation service Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost, and Alfonso Valencia PMCID: PMC1160172 VisANT: data-integrating visual framework for biological networks and modules Zhenjun Hu, Joe Mellor, Jie Wu, Takuji Yamada, Dustin Holloway, and Charles DeLisi PMCID: PMC1160192 MovieMaker: a web server for rapid rendering of protein motions and interactions Rajarshi Maiti, Gary H. Van Domselaar, and David S. Wishart PMCID: PMC1160245 PatchDock and SymmDock: servers for rigid and symmetric docking Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, and Haim J. Wolfson PMCID: PMC1160241 H++: a server for estimating pKas and adding missing hydrogens to macromolecules John C. Gordon, Jonathan B. Myers, Timothy Folta, Valia Shoja, Lenwood S. Heath, and Alexey Onufriev PMCID: PMC1160225 PCE: web tools to compute protein continuum electrostatics Maria A. Miteva, Pierre Tufféry, and Bruno O. Villoutreix PMCID: PMC1160126 DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy Brian D. Halligan, Victor Ruotti, Simon N. Twigger, and Andrew S. Greene PMCID: PMC1160222 The FoldX web server: an online force field Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, and Luis Serrano PMCID: PMC1160148 enoLOGOS: a versatile web tool for energy normalized sequence logos Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, and Panayiotis V. Benos PMCID: PMC1160200 TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis Stein Aerts, Peter Van Loo, Gert Thijs, Herbert Mayer, Rainer de Martin, Yves Moreau, and Bart De Moor PMCID: PMC1160115 AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Lorenz Bülow, and Reinhard Hehl PMCID: PMC1160156 Identifying synonymous regulatory elements in vertebrate genomes Ivan Ovcharenko and Marcelo A. Nobrega PMCID: PMC1160227 CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes Anil G. Jegga, Ashima Gupta, Sivakumar Gowrisankar, Mrunal A. Deshmukh, Steven Connolly, Kevin Finley, and Bruce J. Aronow PMCID: PMC1160246 WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar Guandong Wang, Taotao Yu, and Weixiong Zhang PMCID: PMC1160252 ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters Oleg V. Vishnevsky and Nikolay A. Kolchanov PMCID: PMC1160220 PromoterPlot: a graphical display of promoter similarities by pattern recognition Alessandro Di Cara, Karsten Schmidt, Brian A. Hemmings, and Edward J. Oakeley PMCID: PMC1160174 POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets Matti Kankainen and Liisa Holm PMCID: PMC1160228 P-Match: transcription factor binding site search by combining patterns and weight matrices D. S. Chekmenev, C. Haid, and A. E. Kel PMCID: PMC1160202 T-Reg Comparator: an analysis tool for the comparison of position weight matrices Stefan Roepcke, Steffen Grossmann, Sven Rahmann, and Martin Vingron PMCID: PMC1160266 FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting David L. Corcoran, Eleanor Feingold, and Panayiotis V. Benos PMCID: PMC1160181 CONREAL web server: identification and visualization of conserved transcription factor binding sites Eugene Berezikov, Victor Guryev, and Edwin Cuppen PMCID: PMC1160139 GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses John Besemer and Mark Borodovsky PMCID: PMC1160247 BASys: a web server for automated bacterial genome annotation Gary H. Van Domselaar, Paul Stothard, Savita Shrivastava, Joseph A. Cruz, AnChi Guo, Xiaoli Dong, Paul Lu, Duane Szafron, Russ Greiner, and David S. Wishart PMCID: PMC1160269 BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments Fátima Al-Shahrour, Pablo Minguez, Juan M. Vaquerizas, Lucía Conde, and Joaquín Dopazo PMCID: PMC1160217 AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints Mario Stanke and Burkhard Morgenstern PMCID: PMC1160219 Integrating protein annotation resources through the Distributed Annotation System Páll Ísólfur Ólason PMCID: PMC1160224 MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes Stéphane Cruveiller, Jérôme Le Saux, David Vallenet, Aurélie Lajus, Stéphanie Bocs, and Claudine Médigue PMCID: PMC1160258 nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms Lei Bao, Mi Zhou, and Yan Cui PMCID: PMC1160133 SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis Jinho Yoo, Bonghee Seo, and Yangseok Kim PMCID: PMC1160189 SNP Cutter: a comprehensive tool for SNP PCR–RFLP assay design Ruifang Zhang, Zanhua Zhu, Hongming Zhu, Tu Nguyen, Fengxia Yao, Kun Xia, Desheng Liang, and Chunyu Liu PMCID: PMC1160119 SNPServer: a real-time SNP discovery tool David Savage, Jacqueline Batley, Tim Erwin, Erica Logan, Christopher G. Love, Geraldine A. C. Lim, Emmanuel Mongin, Gary Barker, German C. Spangenberg, and David Edwards PMCID: PMC1160223 ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants Matthias Klaften and Martin Hrabé de Angelis PMCID: PMC1160191 PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes Lucía Conde, Juan M. Vaquerizas, Carles Ferrer-Costa, Xavier de la Cruz, Modesto Orozco, and Joaquín Dopazo PMCID: PMC1165690 AMOD: a morpholino oligonucleotide selection tool Eric W. Klee, Kyong Jin Shim, Michael A. Pickart, Stephen C. Ekker, and Lynda B. M. Ellis PMCID: PMC1160214 GENSTYLE: exploration and analysis of DNA sequences with genomic signature Bernard Fertil, Matthieu Massin, Sylvain Lespinats, Caroline Devic, Philippe Dumee, and Alain Giron PMCID: PMC1160249 PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs Jakob Fredslund, Leif Schauser, Lene H. Madsen, Niels Sandal, and Jens Stougaard PMCID: PMC1160186 Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production Roman Rydzanicz, X. Sharon Zhao, and Philip E. Johnson PMCID: PMC1160141 JCat: a novel tool to adapt codon usage of a target gene to its potential expression host Andreas Grote, Karsten Hiller, Maurice Scheer, Richard Münch, Bernd Nörtemann, Dietmar C. Hempel, and Dieter Jahn PMCID: PMC1160137 Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC Dirk Pöhler, Nadine Werner, Rasmus Steinkamp, and Burkhard Morgenstern PMCID: PMC1160147 PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology Per Eystein Sæbø, Sten Morten Andersen, Jon Myrseth, Jon K. Laerdahl, and Torbjørn Rognes PMCID: PMC1160184 YASS: enhancing the sensitivity of DNA similarity search Laurent Noé and Gregory Kucherov PMCID: PMC1160238 MuPlex: multi-objective multiplex PCR assay design John Rachlin, Chunming Ding, Charles Cantor, and Simon Kasif PMCID: PMC1160138 SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms Steven Ringquist, Christopher Pecoraro, Crystal M. S. Gilchrist, Alexis Styche, William A. Rudert, Panagiotis V. Benos, and Massimo Trucco PMCID: PMC1160243 POWER: PhylOgenetic WEb Repeater—an integrated and user-optimized framework for biomolecular phylogenetic analysis Chung-Yen Lin, Fan-Kai Lin, Chieh Hua Lin, Li-Wei Lai, Hsiu-Jun Hsu, Shu-Hwa Chen, and Chao A. Hsiung PMCID: PMC1160254 PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference Stéphane Guindon, Franck Lethiec, Patrice Duroux, and Olivier Gascuel PMCID: PMC1160113 Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies Sacha A. F. T. van Hijum, Aldert L. Zomer, Oscar P. Kuipers, and Jan Kok PMCID: PMC1160117 FeatureExtract—extraction of sequence annotation made easy Rasmus Wernersson PMCID: PMC1160149 dnaMATE: a consensus melting temperature prediction server for short DNA sequences Alejandro Panjkovich, Tomás Norambuena, and Francisco Melo PMCID: PMC1160140 Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles Eivind Tøstesen, Geir Ivar Jerstad, and Eivind Hovig PMCID: PMC1160185 DINAMelt web server for nucleic acid melting prediction Nicholas R. Markham and Michael Zuker PMCID: PMC1160267 E-RNAi: a web application to design optimized RNAi constructs Zeynep Arziman, Thomas Horn, and Michael Boutros PMCID: PMC1160229 dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference Yuki Naito, Tomoyuki Yamada, Takahiro Matsumiya, Kumiko Ui-Tei, Kaoru Saigo, and Shinichi Morishita PMCID: PMC1160180 T-profiler: scoring the activity of predefined groups of genes using gene expression data André Boorsma, Barrett C. Foat, Daniel Vis, Frans Klis, and Harmen J. Bussemaker PMCID: PMC1160244 GEMS: a web server for biclustering analysis of expression data Chang-Jiun Wu and Simon Kasif PMCID: PMC1160230 RNALOSS: a web server for RNA locally optimal secondary structures P. Clote PMCID: PMC1160143 Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots A. Xayaphoummine, T. Bucher, and H. Isambert PMCID: PMC1160208 OligoWiz 2.0—integrating sequence feature annotation into the design of microarray probes Rasmus Wernersson and Henrik Bjørn Nielsen PMCID: PMC1160160 GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data Juan M. Vaquerizas, Lucía Conde, Patricio Yankilevich, Amaya Cabezón, Pablo Minguez, Ramón Díaz-Uriarte, Fátima Al-Shahrour, Javier Herrero, and Joaquín Dopazo PMCID: PMC1160260 ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics Hee-Joon Chung, Chan Hee Park, Mi Ryung Han, Seokho Lee, Jung Hun Ohn, Jihoon Kim, Jihun Kim, and Ju Han Kim PMCID: PMC1160211 VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data Albert Hsiao, Trey Ideker, Jerrold M. Olefsky, and Shankar Subramaniam PMCID: PMC1160204 PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways Bernhard Mlecnik, Marcel Scheideler, Hubert Hackl, Jürgen Hartler, Fatima Sanchez-Cabo, and Zlatko Trajanoski PMCID: PMC1160152 RACE: Remote Analysis Computation for gene Expression data Michael Psarros, Steffen Heber, Manuela Sick, Gnanasekaran Thoppae, Keith Harshman, and Beate Sick PMCID: PMC1160250 MIDAW: a web tool for statistical analysis of microarray data Chiara Romualdi, Nicola Vitulo, Micky Del Favero, and Gerolamo Lanfranchi PMCID: PMC1160257 The foldalign web server for pairwise structural RNA alignment and mutual motif search Jakob H. Havgaard, Rune B. Lyngsø, and Jan Gorodkin PMCID: PMC1160234 T-STAG: resource and web-interface for tissue-specific transcripts and genes Shobhit Gupta, Martin Vingron, and Stefan A. Haas PMCID: PMC1160111 ASIAN: a web server for inferring a regulatory network framework from gene expression profiles Sachiyo Aburatani, Kousuke Goto, Shigeru Saito, Hiroyuki Toh, and Katsuhisa Horimoto PMCID: PMC1160207 AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts Giovanni Lavorgna, Riccardo Triunfo, Federico Santoni, Ugo Orfanelli, Sara Noci, Alessandro Bulfone, Gianluigi Zanetti, and Giorgio Casari PMCID: PMC1160209 TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang PMCID: PMC1160197 GBA server: EST-based digital gene expression profiling Xin Wu, Michael G. Walker, Jingchu Luo, and Liping Wei PMCID: PMC1160240 OrfPredictor: predicting protein-coding regions in EST-derived sequences Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang PMCID: PMC1160155 ASePCR: alternative splicing electronic RT–PCR in multiple tissues and organs Namshin Kim, Dajeong Lim, Sanghyuk Lee, and Heebal Kim PMCID: PMC1160168 The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs Peter Schattner, Angela N. Brooks, and Todd M. Lowe PMCID: PMC1160127 RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements Cei Abreu-Goodger and Enrique Merino PMCID: PMC1160206 WEBSAGE: a web tool for visual analysis of differentially expressed human SAGE tags Jean Pylouster, Catherine Sénamaud-Beaufort, and Tula Ester Saison-Behmoaras PMCID: PMC1160205 MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence Ventsislav Rusinov, Vesselin Baev, Ivan Nikiforov Minkov, and Martin Tabler PMCID: PMC1160125 miRU: an automated plant miRNA target prediction server Yuanji Zhang PMCID: PMC1160144 AISMIG—an interactive server-side molecule image generator Andreas Bohne-Lang, Wolf-Dieter Groch, and René Ranzinger PMCID: PMC1160199 BRIGEP—the BRIDGE-based genome–transcriptome–proteome browser A. Goesmann, B. Linke, D. Bartels, M. Dondrup, L. Krause, H. Neuweger, S. Oehm, T. Paczian, A. Wilke, and F. Meyer PMCID: PMC1160161 GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists Marco Masseroli, Osvaldo Galati, and Francesco Pinciroli PMCID: PMC1160215 Éclair—a web service for unravelling species origin of sequences sampled from mixed host interfaces Stephen Rudd and Igor V. Tetko PMCID: PMC1160195 The multilocus sequence typing network: mlst.net David M. Aanensen and Brian G. Spratt PMCID: PMC1160176 The bioinformatics resource for oral pathogens Tsute Chen, Kevin Abbey, Wen-jie Deng, and Meng-chuan Cheng PMCID: PMC1160122 WebGestalt: an integrated system for exploring gene sets in various biological contexts Bing Zhang, Stefan Kirov, and Jay Snoddy PMCID: PMC1160236 GenePath: from mutations to genetic networks and back Peter Juvan, Janez Demsar, Gad Shaulsky, and Blaz Zupan PMCID: PMC1160187 Data mining tools for the Saccharomyces cerevisiae morphological database Taro L. Saito, Jun Sese, Yoichiro Nakatani, Fumi Sano, Masashi Yukawa, Yoshikazu Ohya, and Shinichi Morishita PMCID: PMC1160212 GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases M. A. van Driel, K. Cuelenaere, P. P. C. W. Kemmeren, J. A. M. Leunissen, H. G. Brunner, and Gert Vriend PMCID: PMC1160196 Recent additions and improvements to the Onto-Tools Purvesh Khatri, Sivakumar Sellamuthu, Pooja Malhotra, Kashyap Amin, Arina Done, and Sorin Draghici PMCID: PMC1160233 MRS: a fast and compact retrieval system for biological data M. L. Hekkelman and G. Vriend PMCID: PMC1160183 Current Comparative Table (CCT) automates customized searches of dynamic biological databases Benjamin R. Landsteiner, Michael R. Olson, and Robert Rutherford PMCID: PMC1160193 PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts Thomas Goetz and Claus-Wilhelm von der Lieth PMCID: PMC1160190 LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts Holger Maier, Stefanie Döhr, Korbinian Grote, Sean O'Keeffe, Thomas Werner, Martin Hrabé de Angelis, and Ralf Schneider PMCID: PMC1160178 GoPubMed: exploring PubMed with the Gene Ontology Andreas Doms and Michael Schroeder PMCID: PMC1160231 |
