| | Editorial Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W1. Published online 2008 July 1. doi: 10.1093/nar/gkn381.PMCID: PMC2447747 Articles Keeping pace with the data: 2008 update on the Bioinformatics Links Directory Michelle D. Brazas, Joanne A. Fox, Timothy Brown, Scott McMillan, and B. F. Francis Ouellette PMCID: PMC2447757 NCBI BLAST: a better web interface Mark Johnson, Irena Zaretskaya, Yan Raytselis, Yuri Merezhuk, Scott McGinnis, and Thomas L. Madden PMCID: PMC2447716 R-Coffee: a web server for accurately aligning noncoding RNA sequences Sébastien Moretti, Andreas Wilm, Desmond G. Higgins, Ioannis Xenarios, and Cédric Notredame PMCID: PMC2447777 MAGNOLIA: multiple alignment of protein–coding and structural RNA sequences Arnaud Fontaine, Antoine de Monte, and Hélène Touzet PMCID: PMC2447753 SARSA: a web tool for structural alignment of RNA using a structural alphabet Yen-Fu Chang, Yen-Lin Huang, and Chin Lung Lu PMCID: PMC2447761 SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser Thomas P. Walsh, Caleb Webber, Stephen Searle, Shane S. Sturrock, and Geoffrey J. Barton PMCID: PMC2447745 PROMALS3D web server for accurate multiple protein sequence and structure alignments Jimin Pei, Ming Tang, and Nick V. Grishin PMCID: PMC2447800 PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery Maria Garcia-Boronat, Carmen M. Diez-Rivero, Ellis L. Reinherz, and Pedro A. Reche PMCID: PMC2447719 RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes Roberto Mosca and Thomas R. Schneider PMCID: PMC2447786 Superimposé: a 3D structural superposition server Raphael A. Bauer, Philip E. Bourne, Arno Formella, Cornelius Frömmel, Christoph Gille, Andrean Goede, Aysam Guerler, Andreas Hoppe, Ernst-Walter Knapp, Thorsten Pöschel, Burghardt Wittig, Valentin Ziegler, and Robert Preissner PMCID: PMC2447795 SuperPred: drug classification and target prediction Mathias Dunkel, Stefan Günther, Jessica Ahmed, Burghardt Wittig, and Robert Preissner PMCID: PMC2447784 DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture Byungwook Lee and Doheon Lee PMCID: PMC2447808 xREI: a phylo-grammar visualization webserver Lars Barquist and Ian Holmes PMCID: PMC2447789 The Vienna RNA Websuite Andreas R. Gruber, Ronny Lorenz, Stephan H. Bernhart, Richard Neuböck, and Ivo L. Hofacker PMCID: PMC2447809 Software.ncrna.org: web servers for analyses of RNA sequences Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, and Toutai Mituyama PMCID: PMC2447773 WAR: Webserver for aligning structural RNAs Elfar Torarinsson and Stinus Lindgreen PMCID: PMC2447782 NOBAI: a web server for character coding of geometrical and statistical features in RNA structure Vegeir Knudsen and Gustavo Caetano-Anollés PMCID: PMC2447726 RNALogo: a new approach to display structural RNA alignment Tzu-Hao Chang, Jorng-Tzong Horng, and Hsien-Da Huang PMCID: PMC2447718 AsiDesigner: exon-based siRNA design server considering alternative splicing Young-Kyu Park, Seong-Min Park, Young-Chul Choi, Doheon Lee, Misun Won, and Young Joo Kim PMCID: PMC2447810 OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics Zhi John Lu and David H. Mathews PMCID: PMC2447759 TargetRNA: a tool for predicting targets of small RNA action in bacteria Brian Tjaden PMCID: PMC2447797 pssRNAMiner: a plant short small RNA regulatory cascade analysis server Xinbin Dai and Patrick Xuechun Zhao PMCID: PMC2447807 RSAT: regulatory sequence analysis tools Morgane Thomas-Chollier, Olivier Sand, Jean-Valéry Turatsinze, Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohée, and Jacques van Helden PMCID: PMC2447775 ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species Bart Hooghe, Paco Hulpiau, Frans van Roy, and Pieter De Bleser PMCID: PMC2447729 DiRE: identifying distant regulatory elements of co-expressed genes Valer Gotea and Ivan Ovcharenko PMCID: PMC2447744 OREST: the online resource for EST analysis Brigitte Waegele, Thorsten Schmidt, H. Werner Mewes, and Andreas Ruepp PMCID: PMC2447738 CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats Ibtissem Grissa, Gilles Vergnaud, and Christine Pourcel PMCID: PMC2447796 Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design Robert T. Sullivan, Caroline B. Morehouse, NISC Comparative Sequencing Program, and James W. Thomas PMCID: PMC2447791 OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences Olivier Croce, François Chevenet, and Richard Christen PMCID: PMC2447727 Standard and generalized McDonald–Kreitman test: a website to detect selection by comparing different classes of DNA sites Raquel Egea, Sònia Casillas, and Antonio Barbadilla PMCID: PMC2447769 IDT SciTools: a suite for analysis and design of nucleic acid oligomers Richard Owczarzy, Andrey V. Tataurov, Yihe Wu, Jeffrey A. Manthey, Kyle A. McQuisten, Hakeem G. Almabrazi, Kent F. Pedersen, Yuan Lin, Justin Garretson, Neil O. McEntaggart, Chris A. Sailor, Robert B. Dawson, and Andrew S. Peek PMCID: PMC2447751 QUMA: quantification tool for methylation analysis Yuichi Kumaki, Masaaki Oda, and Masaki Okano PMCID: PMC2447804 GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways C. E. Martinez-Guerrero, R. Ciria, C. Abreu-Goodger, G. Moreno-Hagelsieb, and E. Merino PMCID: PMC2447741 The CGView Server: a comparative genomics tool for circular genomes Jason R. Grant and Paul Stothard PMCID: PMC2447734 HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures Naoshi Fukuhara and Takeshi Kawabata PMCID: PMC2447736 TarO: a target optimisation system for structural biology Ian M. Overton, C. A. Johannes van Niekerk, Lester G. Carter, Alice Dawson, David M. A. Martin, Scott Cameron, Stephen A. McMahon, Malcolm F. White, William N. Hunter, James H. Naismith, and Geoffrey J. Barton PMCID: PMC2447720 The Jpred 3 secondary structure prediction server Christian Cole, Jonathan D. Barber, and Geoffrey J. Barton PMCID: PMC2447793 PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation Scott Montgomerie, Joseph A. Cruz, Savita Shrivastava, David Arndt, Mark Berjanskii, and David S. Wishart PMCID: PMC2447806 MolAxis: a server for identification of channels in macromolecules Eitan Yaffe, Dan Fishelovitch, Haim J. Wolfson, Dan Halperin, and Ruth Nussinov PMCID: PMC2447770 LocalMove: computing on-lattice fits for biopolymers Y. Ponty, R. Istrate, E. Porcelli, and P. Clote PMCID: PMC2447748 PharmaGist: a webserver for ligand-based pharmacophore detection Dina Schneidman-Duhovny, Oranit Dror, Yuval Inbar, Ruth Nussinov, and Haim J. Wolfson PMCID: PMC2447755 FireDock: a web server for fast interaction refinement in molecular docking Efrat Mashiach, Dina Schneidman-Duhovny, Nelly Andrusier, Ruth Nussinov, and Haim J. Wolfson PMCID: PMC2447790 The RosettaDock server for local protein–protein docking Sergey Lyskov and Jeffrey J. Gray PMCID: PMC2447798 Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure Grzegorz Koczyk and Igor N. Berezovsky PMCID: PMC2447749 pFlexAna: detecting conformational changes in remotely related proteins Anshul Nigham, Lisa Tucker-Kellogg, Ivana Mihalek, Chandra Verma, and David Hsu PMCID: PMC2447781 soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts Charles A. Lesburg and José S. Duca PMCID: PMC2447792 SEQATOMS: a web tool for identifying missing regions in PDB in sequence context Bernd W. Brandt, Jaap Heringa, and Jack A. M. Leunissen PMCID: PMC2447787 MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, and Haim J. Wolfson PMCID: PMC2447750 KFC Server: interactive forecasting of protein interaction hot spots Steven J. Darnell, Laura LeGault, and Julie C. Mitchell PMCID: PMC2447760 PBEQ-Solver for online visualization of electrostatic potential of biomolecules Sunhwan Jo, Miklos Vargyas, Judit Vasko-Szedlar, Benoît Roux, and Wonpil Im PMCID: PMC2447802 webPIPSA: a web server for the comparison of protein interaction properties Stefan Richter, Anne Wenzel, Matthias Stein, Razif R. Gabdoulline, and Rebecca C. Wade PMCID: PMC2447742 GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries Andrew E. Firth and Wayne M. Patrick PMCID: PMC2447733 The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information Neil F. W. Saunders and Bostjan Kobe PMCID: PMC2447752 E1DS: catalytic site prediction based on 1D signatures of concurrent conservation Ting-Ying Chien, Darby Tien-Hao Chang, Chien-Yu Chen, Yi-Zhong Weng, and Chen-Ming Hsu PMCID: PMC2447799 FFPred: an integrated feature-based function prediction server for vertebrate proteomes A. E. Lobley, T. Nugent, C. A. Orengo, and D. T. Jones PMCID: PMC2447771 3D-Fun: predicting enzyme function from structure Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, and Leszek Rychlewski PMCID: PMC2447717 GEPAS, a web-based tool for microarray data analysis and interpretation Joaquín Tárraga, Ignacio Medina, José Carbonell, Jaime Huerta-Cepas, Pablo Minguez, Eva Alloza, Fátima Al-Shahrour, Susana Vegas-Azcárate, Stefan Goetz, Pablo Escobar, Francisco Garcia-Garcia, Ana Conesa, David Montaner, and Joaquín Dopazo PMCID: PMC2447723 AMIC@: All MIcroarray Clusterings @ once Filippo Geraci, Marco Pellegrini, and M. Elena Renda PMCID: PMC2447730 GeneCAT—novel webtools that combine BLAST and co-expression analyses Marek Mutwil, Jens Øbro, William G. T. Willats, and Staffan Persson PMCID: PMC2447783 Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data Alexander E. Ivliev, Peter A. C. 't Hoen, Michel P. Villerius, Johan T. den Dunnen, and Bernd W. Brandt PMCID: PMC2447788 MADNet: microarray database network web server Igor Šegota, Nenad Bartoniček, and Kristian Vlahoviček PMCID: PMC2447778 GenoWatch: a disease gene mining browser for association study Yan-Hau Chen, Chuan-Kun Liu, Shu-Chuan Chang, Yi-Jung Lin, Ming-Fang Tsai, Yuan-Tsong Chen, and Adam Yao PMCID: PMC2447740 Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments Fátima Al-Shahrour, José Carbonell, Pablo Minguez, Stefan Goetz, Ana Conesa, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, and Joaquín Dopazo PMCID: PMC2447758 ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data Alexey V. Antonov, Thorsten Schmidt, Yu Wang, and Hans W. Mewes PMCID: PMC2447768 Onto-CC: a web server for identifying Gene Ontology conceptual clusters R. Romero-Zaliz, C. del Val, J. P. Cobb, and I. Zwir PMCID: PMC2447763 GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis Qi Zheng and Xiu-Jie Wang PMCID: PMC2447756 PaLS: filtering common literature, biological terms and pathway information Andreu Alibés, Andrés Cañada, and Ramón Díaz-Uriarte PMCID: PMC2447779 SerbGO: searching for the best GO tool J. L. Mosquera and A. Sánchez-Pla PMCID: PMC2447766 The Ontology Lookup Service: more data and better tools for controlled vocabulary queries Richard G. Côté, Philip Jones, Lennart Martens, Rolf Apweiler, and Henning Hermjakob PMCID: PMC2447739 Endeavour update: a web resource for gene prioritization in multiple species Léon-Charles Tranchevent, Roland Barriot, Shi Yu, Steven Van Vooren, Peter Van Loo, Bert Coessens, Bart De Moor, Stein Aerts, and Yves Moreau PMCID: PMC2447805 BioLit: integrating biological literature with databases J. Lynn Fink, Sergey Kushch, Parker R. Williams, and Philip E. Bourne PMCID: PMC2447735 BIOSMILE web search: a web application for annotating biomedical entities and relations Hong-Jie Dai, Chi-Hsin Huang, Ryan T. K. Lin, Richard Tzong-Han Tsai, and Wen-Lian Hsu PMCID: PMC2447743 PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites Dean Cheng, Craig Knox, Nelson Young, Paul Stothard, Sambasivarao Damaraju, and David S. Wishart PMCID: PMC2447794 CoPub: a literature-based keyword enrichment tool for microarray data analysis Raoul Frijters, Bart Heupers, Pieter van Beek, Maurice Bouwhuis, René van Schaik, Jacob de Vlieg, Jan Polman, and Wynand Alkema PMCID: PMC2447728 PIE: an online prediction system for protein–protein interactions from text Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram Sriram, and Byoung-Tak Zhang PMCID: PMC2447724 E3Miner: a text mining tool for ubiquitin-protein ligases Hodong Lee, Gwan-Su Yi, and Jong C. Park PMCID: PMC2447767 KEGG Atlas mapping for global analysis of metabolic pathways Shujiro Okuda, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork, Susumu Goto, and Minoru Kanehisa PMCID: PMC2447737 The University of Minnesota pathway prediction system: predicting metabolic logic Lynda B.M. Ellis, Junfeng Gao, Kathrin Fenner, and Lawrence P. Wackett PMCID: PMC2447765 Comparative Pathway Analyzer—a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms Sebastian Oehm, David Gilbert, Andreas Tauch, Jens Stoye, and Alexander Goesmann PMCID: PMC2447754 Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology Chung-Yen Lin, Chia-Hao Chin, Hsin-Hung Wu, Shu-Hwa Chen, Chin-Wen Ho, and Ming-Tat Ko PMCID: PMC2447731 NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways Sylvain Brohée, Karoline Faust, Gipsi Lima-Mendez, Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, and Jacques van Helden PMCID: PMC2447721 GraphWeb: mining heterogeneous biological networks for gene modules with functional significance Jüri Reimand, Laur Tooming, Hedi Peterson, Priit Adler, and Jaak Vilo PMCID: PMC2447774 ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks Johannes Klein, Stefan Leupold, Richard Münch, Claudia Pommerenke, Thorsten Johl, Uwe Kärst, Lothar Jänsch, Dieter Jahn, and Ida Retter PMCID: PMC2447764 Phylogeny.fr: robust phylogenetic analysis for the non-specialist A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet, F. Chevenet, J.-F. Dufayard, S. Guindon, V. Lefort, M. Lescot, J.-M. Claverie, and O. Gascuel PMCID: PMC2447785 Signature, a web server for taxonomic characterization of sequence samples using signature genes Bas E. Dutilh, Ying He, Maarten L. Hekkelman, and Martijn A. Huynen PMCID: PMC2447722 OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes Li-Wei Jiang, Kuang-Lun Lin, and Chin Lung Lu PMCID: PMC2447762 MassTRIX: mass translator into pathways Karsten Suhre and Philippe Schmitt-Kopplin PMCID: PMC2447776 ISPIDER Central: an integrated database web-server for proteomics Jennifer A. Siepen, Khalid Belhajjame, Julian N. Selley, Suzanne M. Embury, Norman W. Paton, Carole A. Goble, Stephen G. Oliver, Robert Stevens, Lucas Zamboulis, Nigel Martin, Alexandra Poulovassillis, Philip Jones, Richard Côté, Henning Hermjakob, Melissa M. Pentony, David T. Jones, Christine A. Orengo, and Simon J. Hubbard PMCID: PMC2447780 MassNet: a functional annotation service for protein mass spectrometry data Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Seong-Jin Park, Jong-Soon Choi, Seung Il Kim, Jong Bhak, and Sunghoon Lee PMCID: PMC2447811 CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data David S. Wishart, David Arndt, Mark Berjanskii, Peter Tang, Jianjun Zhou, and Guohui Lin PMCID: PMC2447725 IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis Xavier Brochet, Marie-Paule Lefranc, and Véronique Giudicelli PMCID: PMC2447746 NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11 Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, and Morten Nielsen PMCID: PMC2447772 Immune epitope database analysis resource (IEDB-AR) Qing Zhang, Peng Wang, Yohan Kim, Pernille Haste-Andersen, John Beaver, Philip E. Bourne, Huynh-Hoa Bui, Soren Buus, Sune Frankild, Jason Greenbaum, Ole Lund, Claus Lundegaard, Morten Nielsen, Julia Ponomarenko, Alessandro Sette, Zhanyang Zhu, and Bjoern Peters PMCID: PMC2447801 EpiToolKit—a web server for computational immunomics Magdalena Feldhahn, Philipp Thiel, Mathias M. Schuler, Nina Hillen, Stefan Stevanović, Hans-Georg Rammensee, and Oliver Kohlbacher PMCID: PMC2447732 bioNMF: a web-based tool for nonnegative matrix factorization in biology E. Mejía-Roa, P. Carmona-Saez, R. Nogales, C. Vicente, M. Vázquez, X. Y. Yang, C. García, F. Tirado, and A. Pascual-Montano PMCID: PMC2447803 |
