| | Editorial Nucleic Acids Res. 2006 July 1; 34(Web Server issue): W1. Published online 2006 July 14. doi: 10.1093/nar/gkl385.PMCID: PMC1538845 Articles A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory Joanne A. Fox, Scott McMillan, and B. F. Francis Ouellette PMCID: PMC1538876 BLAST: improvements for better sequence analysis Jian Ye, Scott McGinnis, and Thomas L. Madden PMCID: PMC1538791 FISH—family identification of sequence homologues using structure anchored hidden Markov models Jeanette Tångrot, Lixiao Wang, Bo Kågström, and Uwe H. Sauer PMCID: PMC1538871 The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis Markus Rampp, Thomas Soddemann, and Hermann Lederer PMCID: PMC1538907 PreBI: prediction of biological interfaces of proteins in crystals Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, and Haruki Nakamura PMCID: PMC1538861 PAST: fast structure-based searching in the PDB Hanjo Täubig, Arno Buchner, and Jan Griebsch PMCID: PMC1538836 oGNM: online computation of structural dynamics using the Gaussian Network Model Lee-Wei Yang, A. J. Rader, Xiong Liu, Cristopher Jon Jursa, Shann Ching Chen, Hassan A. Karimi, and Ivet Bahar PMCID: PMC1538811 PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence Z. R. Li, H. H. Lin, L. Y. Han, L. Jiang, X. Chen, and Y. Z. Chen PMCID: PMC1538821 PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson–Boltzmann treatment of macromolecule electrostatics Cyril Azuara, Erik Lindahl, Patrice Koehl, Henri Orland, and Marc Delarue PMCID: PMC1538897 PHEPS: web-based pH-dependent Protein Electrostatics Server Alexander A. Kantardjiev and Boris P. Atanasov PMCID: PMC1538834 pKD: re-designing protein pKa values Barbara M. Tynan-Connolly and Jens Erik Nielsen PMCID: PMC1538816 NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis Erik Lindahl, Cyril Azuara, Patrice Koehl, and Marc Delarue PMCID: PMC1538881 UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models Yunho Jang, Jay I. Jeong, and Moon K. Kim PMCID: PMC1538792 PREDITOR: a web server for predicting protein torsion angle restraints Mark V. Berjanskii, Stephen Neal, and David S. Wishart PMCID: PMC1538894 FOLD-RATE: prediction of protein folding rates from amino acid sequence M. Michael Gromiha, A. Mary Thangakani, and S. Selvaraj PMCID: PMC1538837 Protein Peeling 2: a web server to convert protein structures into series of protein units J.-C. Gelly, C. Etchebest, S. Hazout, and A.G. de Brevern PMCID: PMC1538916 ProSAT2—Protein Structure Annotation Server R. R. Gabdoulline, S. Ulbrich, S. Richter, and R. C. Wade PMCID: PMC1538895 FeatureMap3D—a tool to map protein features and sequence conservation onto homologous structures in the PDB Rasmus Wernersson, Kristoffer Rapacki, Hans-Henrik Stærfeldt, Peter Wad Sackett, and Anne Mølgaard PMCID: PMC1538770 ProKware: integrated software for presenting protein structural properties in protein tertiary structures Jui-Hung Hung, Hsien-Da Huang, and Tzong-Yi Lee PMCID: PMC1538827 OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures Edward S. C. Shih, Ruei-chi R. Gan, and Ming-Jing Hwang PMCID: PMC1538888 Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information Sunghoon Lee, Byungwook Lee, Insoo Jang, Sangsoo Kim, and Jong Bhak PMCID: PMC1538878 TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure Blaise T. F. Alako, Daphne Rainey, Harm Nijveen, and Jack A. M. Leunissen PMCID: PMC1538806 TreeDet: a web server to explore sequence space Angel Carro, Michael Tress, David de Juan, Florencio Pazos, Pedro Lopez-Romero, Antonio del Sol, Alfonso Valencia, and Ana M. Rojas PMCID: PMC1538789 CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Joe Dundas, Zheng Ouyang, Jeffery Tseng, Andrew Binkowski, Yaron Turpaz, and Jie Liang PMCID: PMC1538779 Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet M. Tyagi, P. Sharma, C. S. Swamy, F. Cadet, N. Srinivasan, A. G. de Brevern, and B. Offmann PMCID: PMC1538797 ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein–DNA recognition Shandar Ahmad, Hidetoshi Kono, Marcos J. Araúzo-Bravo, and Akinori Sarai PMCID: PMC1538882 3dSS: 3D structural superposition K. Sumathi, P. Ananthalakshmi, M. N. A. Md. Roshan, and K. Sekar PMCID: PMC1538824 MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments Hatice Gulcin Ozer and William C. Ray PMCID: PMC1538782 HHrep: de novo protein repeat detection and the origin of TIM barrels Johannes Söding, Michael Remmert, and Andreas Biegert PMCID: PMC1538828 Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains R. Bhadra, S. Sandhya, K. R. Abhinandan, S. Chakrabarti, R. Sowdhamini, and N. Srinivasan PMCID: PMC1538780 SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace Julien Maupetit, R. Gautier, and Pierre Tufféry PMCID: PMC1538914 (PS)2: protein structure prediction server Chih-Chieh Chen, Jenn-Kang Hwang, and Jinn-Moon Yang PMCID: PMC1538880 KemaDom: a web server for domain prediction using kernel machine with local context Lusheng Chen, Wei Wang, Shaoping Ling, Caiyan Jia, and Fei Wang PMCID: PMC1538912 Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines Alessandro Vullo, Oscar Bortolami, Gianluca Pollastri, and Silvio C. E. Tosatto PMCID: PMC1538873 PONGO: a web server for multiple predictions of all-alpha transmembrane proteins Mauro Amico, Michele Finelli, Ivan Rossi, Andrea Zauli, Arne Elofsson, Håkan Viklund, Gunnar von Heijne, David Jones, Anders Krogh, Piero Fariselli, Pier Luigi Martelli, and Rita Casadio PMCID: PMC1538841 ArchPRED: a template based loop structure prediction server Narcis Fernandez-Fuentes, Jun Zhai, and András Fiser PMCID: PMC1538831 DISULFIND: a disulfide bonding state and cysteine connectivity prediction server Alessio Ceroni, Andrea Passerini, Alessandro Vullo, and Paolo Frasconi PMCID: PMC1538823 DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification F. Ferrè and P. Clote PMCID: PMC1538812 PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins Henry Bigelow and Burkhard Rost PMCID: PMC1538807 transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels J. Waldispühl, Bonnie Berger, Peter Clote, and Jean-Marc Steyaert PMCID: PMC1538872 SVMHC: a server for prediction of MHC-binding peptides Pierre Dönnes and Oliver Kohlbacher PMCID: PMC1538857 REMUS: a tool for identification of unique peptide segments as epitopes Tun-Wen Pai, Margaret Dah-Tsyr Chang, Wen-Shyong Tzou, Bo-Han Su, Pei-Chih Wu, Hao-Teng Chang, and Wei-I Chou PMCID: PMC1538771 AlgPred: prediction of allergenic proteins and mapping of IgE epitopes Sudipto Saha and G. P. S. Raghava PMCID: PMC1538830 pTARGET: a web server for predicting protein subcellular localization Chittibabu Guda PMCID: PMC1538910 DOUTfinder—identification of distant domain outliers using subsignificant sequence similarity Maria Novatchkova, Georg Schneider, Richard Fritz, Frank Eisenhaber, and Alexander Schleiffer PMCID: PMC1538801 TarFisDock: a web server for identifying drug targets with docking approach Honglin Li, Zhenting Gao, Ling Kang, Hailei Zhang, Kun Yang, Kunqian Yu, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Jianhua Shen, Xicheng Wang, and Hualiang Jiang PMCID: PMC1538869 sgTarget: a target selection resource for structural genomics Ana P. C. Rodrigues, Barry J. Grant, and Roderick E. Hubbard PMCID: PMC1538879 HARMONY: a server for the assessment of protein structures G. Pugalenthi, K. Shameer, N. Srinivasan, and R. Sowdhamini PMCID: PMC1538917 RosettaDesign server for protein design Yi Liu and Brian Kuhlman PMCID: PMC1538902 CUPSAT: prediction of protein stability upon point mutations Vijaya Parthiban, M. Michael Gromiha, and Dietmar Schomburg PMCID: PMC1538884 BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences Liangjiang Wang and Susan J. Brown PMCID: PMC1538853 MeMo: a web tool for prediction of protein methylation modifications Hu Chen, Yu Xue, Ni Huang, Xuebiao Yao, and Zhirong Sun PMCID: PMC1538891 SUMOsp: a web server for sumoylation site prediction Yu Xue, Fengfeng Zhou, Chuanhai Fu, Ying Xu, and Xuebiao Yao PMCID: PMC1538802 MODi : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra Sangtae Kim, Seungjin Na, Ji Woong Sim, Heejin Park, Jaeho Jeong, Hokeun Kim, Younghwan Seo, Jawon Seo, Kong-Joo Lee, and Eunok Paek PMCID: PMC1538808 DyNAVacS: an integrative tool for optimized DNA vaccine design Nagarajan Harish, Rekha Gupta, Parul Agarwal, Vinod Scaria, and Beena Pillai PMCID: PMC1538838 NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides Bruce R. Southey, Andinet Amare, Tyler A. Zimmerman, Sandra L. Rodriguez-Zas, and Jonathan V. Sweedler PMCID: PMC1538825 BAGEL: a web-based bacteriocin genome mining tool Anne de Jong, Sacha A. F. T. van Hijum, Jetta J. E. Bijlsma, Jan Kok, and Oscar P. Kuipers PMCID: PMC1538908 GeneAlign: a coding exon prediction tool based on phylogenetical comparisons Shu Ju Hsieh, Chun Yuan Lin, Ning Han Liu, Wei Yuan Chow, and Chuan Yi Tang PMCID: PMC1538901 TOM: a web-based integrated approach for identification of candidate disease genes Simona Rossi, Daniele Masotti, Christine Nardini, Elena Bonora, Giovanni Romeo, Enrico Macii, Luca Benini, and Stefano Volinia PMCID: PMC1538851 WEGO: a web tool for plotting GO annotations Jia Ye, Lin Fang, Hongkun Zheng, Yong Zhang, Jie Chen, Zengjin Zhang, Jing Wang, Shengting Li, Ruiqiang Li, Lars Bolund, and Jun Wang PMCID: PMC1538768 APID: Agile Protein Interaction DataAnalyzer Carlos Prieto and Javier De Las Rivas PMCID: PMC1538863 Protemot: prediction of protein binding sites with automatically extracted geometrical templates Darby Tien-Hao Chang, Yi-Zhong Weng, Jung-Hsin Lin, Ming-Jing Hwang, and Yen-Jen Oyang PMCID: PMC1538868 GRAMM-X public web server for protein–protein docking Andrey Tovchigrechko and Ilya A. Vakser PMCID: PMC1538913 TSEMA: interactive prediction of protein pairings between interacting families José M. G. Izarzugaza, David Juan, Carles Pons, Juan A. G. Ranea, Alfonso Valencia, and Florencio Pazos PMCID: PMC1538787 kinDOCK: a tool for comparative docking of protein kinase ligands Laetitia Martin, Vincent Catherinot, and Gilles Labesse PMCID: PMC1538843 YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms Christopher J. Penkett, James A. Morris, Valerie Wood, and Jürg Bähler PMCID: PMC1538793 The MPI Bioinformatics Toolkit for protein sequence analysis Andreas Biegert, Christian Mayer, Michael Remmert, Johannes Söding, and Andrei N. Lupas PMCID: PMC1538786 VIRGO: computational prediction of gene functions Naveed Massjouni, Corban G. Rivera, and T. M. Murali PMCID: PMC1538839 TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB Chisato Yamasaki, Hiroaki Kawashima, Fusano Todokoro, Yasuhiro Imamizu, Makoto Ogawa, Motohiko Tanino, Takeshi Itoh, Takashi Gojobori, and Tadashi Imanishi PMCID: PMC1538819 DILIMOT: discovery of linear motifs in proteins Victor Neduva and Robert B. Russell PMCID: PMC1538856 MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences Chen-Ming Hsu, Chien-Yu Chen, and Baw-Jhiune Liu PMCID: PMC1538832 ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins Edouard de Castro, Christian J. A. Sigrist, Alexandre Gattiker, Virginie Bulliard, Petra S. Langendijk-Genevaux, Elisabeth Gasteiger, Amos Bairoch, and Nicolas Hulo PMCID: PMC1538847 MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes Shane Neph and Martin Tompa PMCID: PMC1538893 MEME: discovering and analyzing DNA and protein sequence motifs Timothy L. Bailey, Nadya Williams, Chris Misleh, and Wilfred W. Li PMCID: PMC1538909 HHsenser: exhaustive transitive profile search using HMM–HMM comparison Johannes Söding, Michael Remmert, Andreas Biegert, and Andrei N. Lupas PMCID: PMC1538784 JAFA: a protein function annotation meta-server Iddo Friedberg, Tim Harder, and Adam Godzik PMCID: PMC1538919 SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis Han Liang, Weihua Zhou, and Laura F. Landweber PMCID: PMC1538794 Virtual Ribosome—a comprehensive DNA translation tool with support for integration of sequence feature annotation Rasmus Wernersson PMCID: PMC1538826 GenDecoder: genetic code prediction for metazoan mitochondria Federico Abascal, Rafael Zardoya, and David Posada PMCID: PMC1538875 NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes T. Z. DeSantis, Jr, P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, and G. L. Andersen PMCID: PMC1538769 CrossLink: visualization and exploration of sequence relationships between (micro) RNAs Tobias Dezulian, Martin Schaefer, Roland Wiese, Detlef Weigel, and Daniel H. Huson PMCID: PMC1538911 CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments Eckart Bindewald, Thomas D. Schneider, and Bruce A. Shapiro PMCID: PMC1538790 The ARTS web server for aligning RNA tertiary structures Oranit Dror, Ruth Nussinov, and Haim J. Wolfson PMCID: PMC1538835 PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures Yanga Byun and Kyungsook Han PMCID: PMC1538805 RNAMST: efficient and flexible approach for identifying RNA structural homologs Tzu-Hao Chang, Hsien-Da Huang, Tzu-Neng Chuang, Dray-Ming Shien, and Jorng-Tzong Horng PMCID: PMC1538813 RegRNA: an integrated web server for identifying regulatory RNA motifs and elements Hsi-Yuan Huang, Chia-Hung Chien, Kuan-Hua Jen, and Hsien-Da Huang PMCID: PMC1538840 AUGUSTUS: ab initio prediction of alternative transcripts Mario Stanke, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, and Burkhard Morgenstern PMCID: PMC1538822 ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization Tiziana Castrignanò, Raffaella Rizzi, Ivano Giuseppe Talamo, Paolo D'Onorio De Meo, Anna Anselmo, Paola Bonizzoni, and Graziano Pesole PMCID: PMC1538898 ASGS: an alternative splicing graph web service Durgaprasad Bollina, Bernett T. K. Lee, Tin Wee Tan, and Shoba Ranganathan PMCID: PMC1538904 siVirus: web-based antiviral siRNA design software for highly divergent viral sequences Yuki Naito, Kumiko Ui-Tei, Toru Nishikawa, Yutaka Takebe, and Kaoru Saigo PMCID: PMC1538817 RNAhybrid: microRNA target prediction easy, fast and flexible Jan Krüger and Marc Rehmsmeier PMCID: PMC1538877 ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs Jin-Wu Nam, Jinhan Kim, Sung-Kyu Kim, and Byoung-Tak Zhang PMCID: PMC1538778 EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments Ali Masoudi-Nejad, Koichiro Tonomura, Shuichi Kawashima, Yuki Moriya, Masanori Suzuki, Masumi Itoh, Minoru Kanehisa, Takashi Endo, and Susumu Goto PMCID: PMC1538775 jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1 Ming Zhang, Anne-Kathrin Schultz, Charles Calef, Carla Kuiken, Thomas Leitner, Bette Korber, Burkhard Morgenstern, and Mario Stanke PMCID: PMC1538796 BiologicalNetworks: visualization and analysis tool for systems biology Michael Baitaluk, Mayya Sedova, Animesh Ray, and Amarnath Gupta PMCID: PMC1538788 BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, David Montaner, Eva Alloza, Juan M. Vaquerizas, Lucía Conde, Christian Blaschke, Javier Vera, and Joaquín Dopazo PMCID: PMC1538844 CAPweb: a bioinformatics CGH array Analysis Platform Stéphane Liva, Philippe Hupé, Pierre Neuvial, Isabel Brito, Eric Viara, Philippe La Rosa, and Emmanuel Barillot PMCID: PMC1538852 BTW: a web server for Boltzmann time warping of gene expression time series F. Ferrè and P. Clote PMCID: PMC1538860 Next station in microarray data analysis: GEPAS David Montaner, Joaquín Tárraga, Jaime Huerta-Cepas, Jordi Burguet, Juan M. Vaquerizas, Lucía Conde, Pablo Minguez, Javier Vera, Sach Mukherjee, Joan Valls, Miguel A. G. Pujana, Eva Alloza, Javier Herrero, Fátima Al-Shahrour, and Joaquín Dopazo PMCID: PMC1538867 GEPS: the Gene Expression Pattern Scanner Yu-Peng Wang, Liang Liang, Bu-Cong Han, Yu Quan, Xiao Wang, Tao Tao, and Zhi-Liang Ji PMCID: PMC1538815 CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis Johannes Rainer, Fatima Sanchez-Cabo, Gernot Stocker, Alexander Sturn, and Zlatko Trajanoski PMCID: PMC1538903 Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis Iain W. Manfield, Chih-Hung Jen, John W. Pinney, Ioannis Michalopoulos, James R. Bradford, Philip M. Gilmartin, and David R. Westhead PMCID: PMC1538833 JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information Maurice Scheer, Frank Klawonn, Richard Münch, Andreas Grote, Karsten Hiller, Claudia Choi, Ina Koch, Max Schobert, Elisabeth Härtig, Ulrich Klages, and Dieter Jahn PMCID: PMC1538798 Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases Jeffrey G. Mandell and Carlos F. Barbas, III PMCID: PMC1538883 TFBScluster web server for the identification of mammalian composite regulatory elements Ian J. Donaldson and Berthold Göttgens PMCID: PMC1538905 VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees Jan Grau, Irad Ben-Gal, Stefan Posch, and Ivo Grosse PMCID: PMC1538886 POXO: a web-enabled tool series to discover transcription factor binding sites Matti Kankainen, Petri Pehkonen, Päivi Rosenstöm, Petri Törönen, Garry Wong, and Liisa Holm PMCID: PMC1538773 Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm T. Waleev, D. Shtokalo, T. Konovalova, N. Voss, E. Cheremushkin, P. Stegmaier, O. Kel-Margoulis, E. Wingender, and A. Kel PMCID: PMC1538785 jPREdictor: a versatile tool for the prediction of cis-regulatory elements Thomas Fiedler and Marc Rehmsmeier PMCID: PMC1538890 CEAS: cis-regulatory element annotation system Xuwo Ji, Wei Li, Jun Song, Liping Wei, and X. Shirley Liu PMCID: PMC1538818 Stubb: a program for discovery and analysis of cis-regulatory modules Saurabh Sinha, Yupu Liang, and Eric Siggia PMCID: PMC1538799 NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors Peter Luykx, Ivan V. Bajić, and Sawsan Khuri PMCID: PMC1538820 MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes Giulio Pavesi, Paolo Mereghetti, Federico Zambelli, Marco Stefani, Giancarlo Mauri, and Graziano Pesole PMCID: PMC1538899 CRSD: a comprehensive web server for composite regulatory signature discovery Chun-Chi Liu, Chin-Chung Lin, Wen-Shyen E. Chen, Hsuan-Yu Chen, Pei-Chun Chang, Jeremy J.W. Chen, and Pan-Chyr Yang PMCID: PMC1538777 PromAn: an integrated knowledge-based web server dedicated to promoter analysis Aurélie Lardenois, Frédéric Chalmel, Laurent Bianchetti, José-Alain Sahel, Thierry Léveillard, and Olivier Poch PMCID: PMC1538850 iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species Sarita Ranjan, Jayshree Seshadri, Vaibhav Vindal, Sailu Yellaboina, and Akash Ranjan PMCID: PMC1538900 TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites M. Tech, B. Morgenstern, and P. Meinicke PMCID: PMC1538874 FeatureScan: revealing property-dependent similarity of nucleotide sequences Igor V. Deyneko, Björn Bredohl, Daniel Wesely, Yulia M. Kalybaeva, Alexander E. Kel, Helmut Blöcker, and Gerhard Kauer PMCID: PMC1538849 Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment Timo Lassmann and Erik L. L. Sonnhammer PMCID: PMC1538774 PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments Sébastien Moretti, Frédéric Reinier, Olivier Poirot, Fabrice Armougom, Stéphane Audic, Vladimir Keduas, and Cédric Notredame PMCID: PMC1538918 Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee Fabrice Armougom, Sébastien Moretti, Olivier Poirot, Stéphane Audic, Pierre Dumas, Basile Schaeli, Vladimir Keduas, and Cedric Notredame PMCID: PMC1538866 PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments Mikita Suyama, David Torrents, and Peer Bork PMCID: PMC1538804 AliWABA: alignment on the web through an A-Bruijn approach Neil C. Jones, Degui Zhi, and Benjamin J. Raphael PMCID: PMC1538870 FootPrinter3: phylogenetic footprinting in partially alignable sequences Fei Fang and Mathieu Blanchette PMCID: PMC1538810 PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes Lucía Conde, Juan M. Vaquerizas, Hernán Dopazo, Leonardo Arbiza, Joke Reumers, Frederic Rousseau, Joost Schymkowitz, and Joaquín Dopazo PMCID: PMC1538854 New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate Purvesh Khatri, Valmik Desai, Adi L. Tarca, Sivakumar Sellamuthu, Derek E. Wildman, Roberto Romero, and Sorin Draghici PMCID: PMC1538776 PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA Sònia Casillas and Antonio Barbadilla PMCID: PMC1538800 FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization Hsiang-Yu Yuan, Jen-Jie Chiou, Wen-Hsien Tseng, Chia-Hung Liu, Chuan-Kun Liu, Yi-Jung Lin, Hui-Hung Wang, Adam Yao, Yuan-Tsong Chen, and Chun-Nan Hsu PMCID: PMC1538865 SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences Areum Han, Hyo Jin Kang, Yoobok Cho, Sunghoon Lee, Young Joo Kim, and Sungsam Gong PMCID: PMC1538855 Applications for protein sequence–function evolution data: mRNA/protein expression analysis and coding SNP scoring tools Paul D. Thomas, Anish Kejariwal, Nan Guo, Huaiyu Mi, Michael J. Campbell, Anushya Muruganujan, and Betty Lazareva-Ulitsky PMCID: PMC1538848 SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes Reidar Andreson, Tarmo Puurand, and Maido Remm PMCID: PMC1538889 SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery Erica Jewell, Andrew Robinson, David Savage, Tim Erwin, Christopher G. Love, Geraldine A. C. Lim, Xi Li, Jacqueline Batley, German C. Spangenberg, and David Edwards PMCID: PMC1538772 MutScreener: primer design tool for PCR-direct sequencing Fengxia Yao, Ruifang Zhang, Zanhua Zhu, Kun Xia, and Chunyu Liu PMCID: PMC1538803 PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome Tomoyuki Yamada, Haruhiko Soma, and Shinichi Morishita PMCID: PMC1538814 GeMprospector—online design of cross-species genetic marker candidates in legumes and grasses Jakob Fredslund, Lene H. Madsen, Birgit K. Hougaard, Niels Sandal, Jens Stougaard, David Bertioli, and Leif Schauser PMCID: PMC1538858 QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences Oleg Kikin, Lawrence D'Antonio, and Paramjeet S Bagga PMCID: PMC1538864 Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences Vinod Scaria, Manoj Hariharan, Amit Arora, and Souvik Maiti PMCID: PMC1538896 GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences Feng Gao and Chun-Ting Zhang PMCID: PMC1538862 CorGen—measuring and generating long-range correlations for DNA sequence analysis Philipp W. Messer and Peter F. Arndt PMCID: PMC1538783 SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges Ying Chih Lin, Chin Lung Lu, Ying-Chuan Liu, and Chuan Yi Tang PMCID: PMC1538842 ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online David Posada PMCID: PMC1538795 The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses Jörg Schultz, Tobias Müller, Marco Achtziger, Philipp N. Seibel, Thomas Dandekar, and Matthias Wolf PMCID: PMC1538906 PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats Gábor Tóth, Gábor Deák, Endre Barta, and György B. Kiss PMCID: PMC1538846 The Path-A metabolic pathway prediction web server Luca Pireddu, Duane Szafron, Paul Lu, and Russell Greiner PMCID: PMC1538809 KOBAS server: a web-based platform for automated annotation and pathway identification Jianmin Wu, Xizeng Mao, Tao Cai, Jingchu Luo, and Liping Wei PMCID: PMC1538915 metaSHARK: a WWW platform for interactive exploration of metabolic networks Christopher Hyland, John W. Pinney, Glenn A. McConkey, and David R. Westhead PMCID: PMC1538829 Taverna: a tool for building and running workflows of services Duncan Hull, Katy Wolstencroft, Robert Stevens, Carole Goble, Mathew R. Pocock, Peter Li, and Tom Oinn PMCID: PMC1538887 GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface Alexander Loß, Roland Stenutz, Eberhard Schwarzer, and Claus-W. von der Lieth PMCID: PMC1538781 FAF-Drugs: free ADME/tox filtering of compound collections Maria A. Miteva, Stephanie Violas, Matthieu Montes, David Gomez, Pierre Tuffery, and Bruno O. Villoutreix PMCID: PMC1538885 HubMed: a web-based biomedical literature search interface Alfred D. Eaton PMCID: PMC1538859 botXminer: mining biomedical literature with a new web-based application Uma Mudunuri, Robert Stephens, David Bruining, David Liu, and Frank J. Lebeda PMCID: PMC1538892 |
