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  		Contents: Volume 36, Web Server issue, 1 July 2008   [Index by Author] 

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Editorial Back

Gary Benson
Editorial
Nucl. Acids Res. 2008 36: W1; doi:10.1093/nar/gkn381 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Articles Back

Michelle D. Brazas, Joanne A. Fox, Timothy Brown, Scott McMillan, and B. F. Francis Ouellette
Keeping pace with the data: 2008 update on the Bioinformatics Links Directory
Nucl. Acids Res. 2008 36: W2-W4; doi:10.1093/nar/gkn399 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Web Server Summaries]  

Mark Johnson, Irena Zaretskaya, Yan Raytselis, Yuri Merezhuk, Scott McGinnis, and Thomas L. Madden
NCBI BLAST: a better web interface
Nucleic Acids Research Advance Access published on April 24, 2008
Nucl. Acids Res. 2008 36: W5-W9; doi:10.1093/nar/gkn201 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sébastien Moretti, Andreas Wilm, Desmond G. Higgins, Ioannis Xenarios, and Cédric Notredame
R-Coffee: a web server for accurately aligning noncoding RNA sequences
Nucleic Acids Research Advance Access published on May 15, 2008
Nucl. Acids Res. 2008 36: W10-W13; doi:10.1093/nar/gkn278 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Arnaud Fontaine, Antoine de Monte, and Hélène Touzet
MAGNOLIA: multiple alignment of protein–coding and structural RNA sequences
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: W14-W18; doi:10.1093/nar/gkn321 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yen-Fu Chang, Yen-Lin Huang, and Chin Lung Lu
SARSA: a web tool for structural alignment of RNA using a structural alphabet
Nucleic Acids Research Advance Access published on May 23, 2008
Nucl. Acids Res. 2008 36: W19-W24; doi:10.1093/nar/gkn327 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Thomas P. Walsh, Caleb Webber, Stephen Searle, Shane S. Sturrock, and Geoffrey J. Barton
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
Nucleic Acids Research Advance Access published on May 24, 2008
Nucl. Acids Res. 2008 36: W25-W29; doi:10.1093/nar/gkn320 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jimin Pei, Ming Tang, and Nick V. Grishin
PROMALS3D web server for accurate multiple protein sequence and structure alignments
Nucleic Acids Research Advance Access published on May 24, 2008
Nucl. Acids Res. 2008 36: W30-W34; doi:10.1093/nar/gkn322 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Maria Garcia-Boronat, Carmen M. Diez-Rivero, Ellis L. Reinherz, and Pedro A. Reche
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery
Nucleic Acids Research Advance Access published on April 27, 2008
Nucl. Acids Res. 2008 36: W35-W41; doi:10.1093/nar/gkn211 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Roberto Mosca and Thomas R. Schneider
RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes
Nucleic Acids Research Advance Access published on May 6, 2008
Nucl. Acids Res. 2008 36: W42-W46; doi:10.1093/nar/gkn197 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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
Superimposé: a 3D structural superposition server
Nucleic Acids Research Advance Access published on May 20, 2008
Nucl. Acids Res. 2008 36: W47-W54; doi:10.1093/nar/gkn285 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mathias Dunkel, Stefan Günther, Jessica Ahmed, Burghardt Wittig, and Robert Preissner
SuperPred: drug classification and target prediction
Nucleic Acids Research Advance Access published on May 22, 2008
Nucl. Acids Res. 2008 36: W55-W59; doi:10.1093/nar/gkn307 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Byungwook Lee and Doheon Lee
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture
Nucleic Acids Research Advance Access published on April 14, 2008
Nucl. Acids Res. 2008 36: W60-W64; doi:10.1093/nar/gkn172 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lars Barquist and Ian Holmes
xREI: a phylo-grammar visualization webserver
Nucleic Acids Research Advance Access published on June 3, 2008
Nucl. Acids Res. 2008 36: W65-W69; doi:10.1093/nar/gkn283 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andreas R. Gruber, Ronny Lorenz, Stephan H. Bernhart, Richard Neuböck, and Ivo L. Hofacker
The Vienna RNA Websuite
Nucleic Acids Research Advance Access published on April 19, 2008
Nucl. Acids Res. 2008 36: W70-W74; doi:10.1093/nar/gkn188 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, and Toutai Mituyama
Software.ncrna.org: web servers for analyses of RNA sequences
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: W75-W78; doi:10.1093/nar/gkn222 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Elfar Torarinsson and Stinus Lindgreen
WAR: Webserver for aligning structural RNAs
Nucleic Acids Research Advance Access published on May 20, 2008
Nucl. Acids Res. 2008 36: W79-W84; doi:10.1093/nar/gkn275 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Vegeir Knudsen and Gustavo Caetano-Anollés
NOBAI: a web server for character coding of geometrical and statistical features in RNA structure
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: W85-W90; doi:10.1093/nar/gkn220 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tzu-Hao Chang, Jorng-Tzong Horng, and Hsien-Da Huang
RNALogo: a new approach to display structural RNA alignment
Nucleic Acids Research Advance Access published on May 21, 2008
Nucl. Acids Res. 2008 36: W91-W96; doi:10.1093/nar/gkn258 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Young-Kyu Park, Seong-Min Park, Young-Chul Choi, Doheon Lee, Misun Won, and Young Joo Kim
AsiDesigner: exon-based siRNA design server considering alternative splicing
Nucleic Acids Research Advance Access published on May 14, 2008
Nucl. Acids Res. 2008 36: W97-W103; doi:10.1093/nar/gkn280 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zhi John Lu and David H. Mathews
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics
Nucleic Acids Research Advance Access published on May 19, 2008
Nucl. Acids Res. 2008 36: W104-W108; doi:10.1093/nar/gkn250 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Brian Tjaden
TargetRNA: a tool for predicting targets of small RNA action in bacteria
Nucleic Acids Research Advance Access published on May 13, 2008
Nucl. Acids Res. 2008 36: W109-W113; doi:10.1093/nar/gkn264 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Xinbin Dai and Patrick Xuechun Zhao
pssRNAMiner: a plant short small RNA regulatory cascade analysis server
Nucleic Acids Research Advance Access published on May 12, 2008
Nucl. Acids Res. 2008 36: W114-W118; doi:10.1093/nar/gkn297 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Morgane Thomas-Chollier, Olivier Sand, Jean-Valéry Turatsinze, Rekin's Janky, Matthieu Defrance, Eric Vervisch, Sylvain Brohée, and Jacques van Helden
RSAT: regulatory sequence analysis tools
Nucleic Acids Research Advance Access published on May 21, 2008
Nucl. Acids Res. 2008 36: W119-W127; doi:10.1093/nar/gkn304 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bart Hooghe, Paco Hulpiau, Frans van Roy, and Pieter De Bleser
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species
Nucleic Acids Research Advance Access published on May 3, 2008
Nucl. Acids Res. 2008 36: W128-W132; doi:10.1093/nar/gkn195 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Valer Gotea and Ivan Ovcharenko
DiRE: identifying distant regulatory elements of co-expressed genes
Nucleic Acids Research Advance Access published on May 17, 2008
Nucl. Acids Res. 2008 36: W133-W139; doi:10.1093/nar/gkn300 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Brigitte Waegele, Thorsten Schmidt, H. Werner Mewes, and Andreas Ruepp
OREST: the online resource for EST analysis
Nucleic Acids Research Advance Access published on May 7, 2008
Nucl. Acids Res. 2008 36: W140-W144; doi:10.1093/nar/gkn253 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ibtissem Grissa, Gilles Vergnaud, and Christine Pourcel
CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats
Nucleic Acids Research Advance Access published on April 28, 2008
Nucl. Acids Res. 2008 36: W145-W148; doi:10.1093/nar/gkn228 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Robert T. Sullivan, Caroline B. Morehouse, NISC Comparative Sequencing Program, and James W. Thomas
Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: W149-W153; doi:10.1093/nar/gkn293 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Olivier Croce, François Chevenet, and Richard Christen
OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: W154-W156; doi:10.1093/nar/gkn221 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Raquel Egea, Sònia Casillas, and Antonio Barbadilla
Standard and generalized McDonald–Kreitman test: a website to detect selection by comparing different classes of DNA sites
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: W157-W162; doi:10.1093/nar/gkn337 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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
IDT SciTools: a suite for analysis and design of nucleic acid oligomers
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: W163-W169; doi:10.1093/nar/gkn198 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yuichi Kumaki, Masaaki Oda, and Masaki Okano
QUMA: quantification tool for methylation analysis
Nucleic Acids Research Advance Access published on May 16, 2008
Nucl. Acids Res. 2008 36: W170-W175; doi:10.1093/nar/gkn294 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

C. E. Martinez-Guerrero, R. Ciria, C. Abreu-Goodger, G. Moreno-Hagelsieb, and E. Merino
GeConT 2: gene context analysis for orthologous proteins, conserved domains and metabolic pathways
Nucleic Acids Research Advance Access published on May 29, 2008
Nucl. Acids Res. 2008 36: W176-W180; doi:10.1093/nar/gkn330 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jason R. Grant and Paul Stothard
The CGView Server: a comparative genomics tool for circular genomes
Nucleic Acids Research Advance Access published on April 14, 2008
Nucl. Acids Res. 2008 36: W181-W184; doi:10.1093/nar/gkn179 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Naoshi Fukuhara and Takeshi Kawabata
HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures
Nucleic Acids Research Advance Access published on April 28, 2008
Nucl. Acids Res. 2008 36: W185-W189; doi:10.1093/nar/gkn218 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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
TarO: a target optimisation system for structural biology
Nucleic Acids Research Advance Access published on April 2, 2008
Nucl. Acids Res. 2008 36: W190-W196; doi:10.1093/nar/gkn141 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Christian Cole, Jonathan D. Barber, and Geoffrey J. Barton
The Jpred 3 secondary structure prediction server
Nucleic Acids Research Advance Access published on May 7, 2008
Nucl. Acids Res. 2008 36: W197-W201; doi:10.1093/nar/gkn238 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Scott Montgomerie, Joseph A. Cruz, Savita Shrivastava, David Arndt, Mark Berjanskii, and David S. Wishart
PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation
Nucleic Acids Research Advance Access published on May 15, 2008
Nucl. Acids Res. 2008 36: W202-W209; doi:10.1093/nar/gkn255 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Eitan Yaffe, Dan Fishelovitch, Haim J. Wolfson, Dan Halperin, and Ruth Nussinov
MolAxis: a server for identification of channels in macromolecules
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: W210-W215; doi:10.1093/nar/gkn223 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Y. Ponty, R. Istrate, E. Porcelli, and P. Clote
LocalMove: computing on-lattice fits for biopolymers
Nucleic Acids Research Advance Access published on June 13, 2008
Nucl. Acids Res. 2008 36: W216-W222; doi:10.1093/nar/gkn367 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Dina Schneidman-Duhovny, Oranit Dror, Yuval Inbar, Ruth Nussinov, and Haim J. Wolfson
PharmaGist: a webserver for ligand-based pharmacophore detection
Nucleic Acids Research Advance Access published on April 19, 2008
Nucl. Acids Res. 2008 36: W223-W228; doi:10.1093/nar/gkn187 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Efrat Mashiach, Dina Schneidman-Duhovny, Nelly Andrusier, Ruth Nussinov, and Haim J. Wolfson
FireDock: a web server for fast interaction refinement in molecular docking
Nucleic Acids Research Advance Access published on April 19, 2008
Nucl. Acids Res. 2008 36: W229-W232; doi:10.1093/nar/gkn186 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sergey Lyskov and Jeffrey J. Gray
The RosettaDock server for local protein–protein docking
Nucleic Acids Research Advance Access published on April 28, 2008
Nucl. Acids Res. 2008 36: W233-W238; doi:10.1093/nar/gkn216 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Grzegorz Koczyk and Igor N. Berezovsky
Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure
Nucleic Acids Research Advance Access published on May 23, 2008
Nucl. Acids Res. 2008 36: W239-W245; doi:10.1093/nar/gkn326 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Anshul Nigham, Lisa Tucker-Kellogg, Ivana Mihalek, Chandra Verma, and David Hsu
pFlexAna: detecting conformational changes in remotely related proteins
Nucleic Acids Research Advance Access published on May 13, 2008
Nucl. Acids Res. 2008 36: W246-W251; doi:10.1093/nar/gkn259 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Charles A. Lesburg and José S. Duca
soaPDB: a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts
Nucleic Acids Research Advance Access published on May 16, 2008
Nucl. Acids Res. 2008 36: W252-W254; doi:10.1093/nar/gkn270 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bernd W. Brandt, Jaap Heringa, and Jack A. M. Leunissen
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context
Nucleic Acids Research Advance Access published on May 7, 2008
Nucl. Acids Res. 2008 36: W255-W259; doi:10.1093/nar/gkn237 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, and Haim J. Wolfson
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions
Nucleic Acids Research Advance Access published on May 8, 2008
Nucl. Acids Res. 2008 36: W260-W264; doi:10.1093/nar/gkn185 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Steven J. Darnell, Laura LeGault, and Julie C. Mitchell
KFC Server: interactive forecasting of protein interaction hot spots
Nucleic Acids Research Advance Access published on June 6, 2008
Nucl. Acids Res. 2008 36: W265-W269; doi:10.1093/nar/gkn346 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sunhwan Jo, Miklos Vargyas, Judit Vasko-Szedlar, Benoît Roux, and Wonpil Im
PBEQ-Solver for online visualization of electrostatic potential of biomolecules
Nucleic Acids Research Advance Access published on May 28, 2008
Nucl. Acids Res. 2008 36: W270-W275; doi:10.1093/nar/gkn314 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Stefan Richter, Anne Wenzel, Matthias Stein, Razif R. Gabdoulline, and Rebecca C. Wade
webPIPSA: a web server for the comparison of protein interaction properties
Nucleic Acids Research Advance Access published on April 17, 2008
Nucl. Acids Res. 2008 36: W276-W280; doi:10.1093/nar/gkn181 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andrew E. Firth and Wayne M. Patrick
GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries
Nucleic Acids Research Advance Access published on April 28, 2008
Nucl. Acids Res. 2008 36: W281-W285; doi:10.1093/nar/gkn226 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Neil F. W. Saunders and Bostjan Kobe
The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information
Nucleic Acids Research Advance Access published on May 13, 2008
Nucl. Acids Res. 2008 36: W286-W290; doi:10.1093/nar/gkn279 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ting-Ying Chien, Darby Tien-Hao Chang, Chien-Yu Chen, Yi-Zhong Weng, and Chen-Ming Hsu
E1DS: catalytic site prediction based on 1D signatures of concurrent conservation
Nucleic Acids Research Advance Access published on June 4, 2008
Nucl. Acids Res. 2008 36: W291-W296; doi:10.1093/nar/gkn324 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

A. E. Lobley, T. Nugent, C. A. Orengo, and D. T. Jones
FFPred: an integrated feature-based function prediction server for vertebrate proteomes
Nucleic Acids Research Advance Access published on May 7, 2008
Nucl. Acids Res. 2008 36: W297-W302; doi:10.1093/nar/gkn193 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, and Leszek Rychlewski
3D-Fun: predicting enzyme function from structure
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: W303-W307; doi:10.1093/nar/gkn308 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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
GEPAS, a web-based tool for microarray data analysis and interpretation
Nucleic Acids Research Advance Access published on May 28, 2008
Nucl. Acids Res. 2008 36: W308-W314; doi:10.1093/nar/gkn303 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Filippo Geraci, Marco Pellegrini, and M. Elena Renda
AMIC@: All MIcroarray Clusterings @ once
Nucleic Acids Research Advance Access published on May 13, 2008
Nucl. Acids Res. 2008 36: W315-W319; doi:10.1093/nar/gkn265 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marek Mutwil, Jens Øbro, William G. T. Willats, and Staffan Persson
GeneCAT—novel webtools that combine BLAST and co-expression analyses
Nucleic Acids Research Advance Access published on May 14, 2008
Nucl. Acids Res. 2008 36: W320-W326; doi:10.1093/nar/gkn292 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Alexander E. Ivliev, Peter A. C. 't Hoen, Michel P. Villerius, Johan T. den Dunnen, and Bernd W. Brandt
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data
Nucleic Acids Research Advance Access published on May 7, 2008
Nucl. Acids Res. 2008 36: W327-W331; doi:10.1093/nar/gkn213 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Igor Segota, Nenad Bartonicek, and Kristian Vlahovicek
MADNet: microarray database network web server
Nucleic Acids Research Advance Access published on May 14, 2008
Nucl. Acids Res. 2008 36: W332-W335; doi:10.1093/nar/gkn289 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yan-Hau Chen, Chuan-Kun Liu, Shu-Chuan Chang, Yi-Jung Lin, Ming-Fang Tsai, Yuan-Tsong Chen, and Adam Yao
GenoWatch: a disease gene mining browser for association study
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: W336-W340; doi:10.1093/nar/gkn214 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fátima Al-Shahrour, José Carbonell, Pablo Minguez, Stefan Goetz, Ana Conesa, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, and Joaquín Dopazo
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: W341-W346; doi:10.1093/nar/gkn318 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexey V. Antonov, Thorsten Schmidt, Yu Wang, and Hans W. Mewes
ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
Nucleic Acids Research Advance Access published on May 6, 2008
Nucl. Acids Res. 2008 36: W347-W351; doi:10.1093/nar/gkn239 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

R. Romero-Zaliz, C. del Val, J. P. Cobb, and I. Zwir
Onto-CC: a web server for identifying Gene Ontology conceptual clusters
Nucleic Acids Research Advance Access published on June 10, 2008
Nucl. Acids Res. 2008 36: W352-W357; doi:10.1093/nar/gkn323 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Qi Zheng and Xiu-Jie Wang
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
Nucleic Acids Research Advance Access published on May 16, 2008
Nucl. Acids Res. 2008 36: W358-W363; doi:10.1093/nar/gkn276 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Andreu Alibés, Andrés Cañada, and Ramón Díaz-Uriarte
PaLS: filtering common literature, biological terms and pathway information
Nucleic Acids Research Advance Access published on May 8, 2008
Nucl. Acids Res. 2008 36: W364-W367; doi:10.1093/nar/gkn251 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

J. L. Mosquera and A. Sánchez-Pla
SerbGO: searching for the best GO tool
Nucleic Acids Research Advance Access published on May 14, 2008
Nucl. Acids Res. 2008 36: W368-W371; doi:10.1093/nar/gkn256 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Richard G. Côté, Philip Jones, Lennart Martens, Rolf Apweiler, and Henning Hermjakob
The Ontology Lookup Service: more data and better tools for controlled vocabulary queries
Nucleic Acids Research Advance Access published on May 8, 2008
Nucl. Acids Res. 2008 36: W372-W376; doi:10.1093/nar/gkn252 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Léon-Charles Tranchevent, Roland Barriot, Shi Yu, Steven Van Vooren, Peter Van Loo, Bert Coessens, Bart De Moor, Stein Aerts, and Yves Moreau
ENDEAVOUR update: a web resource for gene prioritization in multiple species
Nucleic Acids Research Advance Access published on May 28, 2008
Nucl. Acids Res. 2008 36: W377-W384; doi:10.1093/nar/gkn325 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

J. Lynn Fink, Sergey Kushch, Parker R. Williams, and Philip E. Bourne
BioLit: integrating biological literature with databases
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: W385-W389; doi:10.1093/nar/gkn317 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hong-Jie Dai, Chi-Hsin Huang, Ryan T. K. Lin, Richard Tzong-Han Tsai, and Wen-Lian Hsu
BIOSMILE web search: a web application for annotating biomedical entities and relations
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: W390-W398; doi:10.1093/nar/gkn319 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Dean Cheng, Craig Knox, Nelson Young, Paul Stothard, Sambasivarao Damaraju, and David S. Wishart
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites
Nucleic Acids Research Advance Access published on May 16, 2008
Nucl. Acids Res. 2008 36: W399-W405; doi:10.1093/nar/gkn296 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Raoul Frijters, Bart Heupers, Pieter van Beek, Maurice Bouwhuis, René van Schaik, Jacob de Vlieg, Jan Polman, and Wynand Alkema
CoPub: a literature-based keyword enrichment tool for microarray data analysis
Nucleic Acids Research Advance Access published on April 28, 2008
Nucl. Acids Res. 2008 36: W406-W410; doi:10.1093/nar/gkn215 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sun Kim, Soo-Yong Shin, In-Hee Lee, Soo-Jin Kim, Ram Sriram, and Byoung-Tak Zhang
PIE: an online prediction system for protein–protein interactions from text
Nucleic Acids Research Advance Access published on May 28, 2008
Nucl. Acids Res. 2008 36: W411-W415; doi:10.1093/nar/gkn281 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hodong Lee, Gwan-Su Yi, and Jong C. Park
E3Miner: a text mining tool for ubiquitin-protein ligases
Nucleic Acids Research Advance Access published on May 15, 2008
Nucl. Acids Res. 2008 36: W416-W422; doi:10.1093/nar/gkn286 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Shujiro Okuda, Takuji Yamada, Masami Hamajima, Masumi Itoh, Toshiaki Katayama, Peer Bork, Susumu Goto, and Minoru Kanehisa
KEGG Atlas mapping for global analysis of metabolic pathways
Nucleic Acids Research Advance Access published on May 13, 2008
Nucl. Acids Res. 2008 36: W423-W426; doi:10.1093/nar/gkn282 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lynda B.M. Ellis, Junfeng Gao, Kathrin Fenner, and Lawrence P. Wackett
The University of Minnesota pathway prediction system: predicting metabolic logic
Nucleic Acids Research Advance Access published on June 4, 2008
Nucl. Acids Res. 2008 36: W427-W432; doi:10.1093/nar/gkn315 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sebastian Oehm, David Gilbert, Andreas Tauch, Jens Stoye, and Alexander Goesmann
Comparative Pathway Analyzer—a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms
Nucleic Acids Research Advance Access published on June 6, 2008
Nucl. Acids Res. 2008 36: W433-W437; doi:10.1093/nar/gkn284 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Chung-Yen Lin, Chia-Hao Chin, Hsin-Hung Wu, Shu-Hwa Chen, Chin-Wen Ho, and Ming-Tat Ko
Hubba: hub objects analyzer—a framework of interactome hubs identification for network biology
Nucleic Acids Research Advance Access published on May 24, 2008
Nucl. Acids Res. 2008 36: W438-W443; doi:10.1093/nar/gkn257 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sylvain Brohée, Karoline Faust, Gipsi Lima-Mendez, Olivier Sand, Rekin's Janky, Gilles Vanderstocken, Yves Deville, and Jacques van Helden
NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
Nucleic Acids Research Advance Access published on June 4, 2008
Nucl. Acids Res. 2008 36: W444-W451; doi:10.1093/nar/gkn336 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jüri Reimand, Laur Tooming, Hedi Peterson, Priit Adler, and Jaak Vilo
GraphWeb: mining heterogeneous biological networks for gene modules with functional significance
Nucleic Acids Research Advance Access published on May 6, 2008
Nucl. Acids Res. 2008 36: W452-W459; doi:10.1093/nar/gkn230 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Johannes Klein, Stefan Leupold, Richard Münch, Claudia Pommerenke, Thorsten Johl, Uwe Kärst, Lothar Jänsch, Dieter Jahn, and Ida Retter
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: W460-W464; doi:10.1093/nar/gkn217 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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
Phylogeny.fr: robust phylogenetic analysis for the non-specialist
Nucleic Acids Research Advance Access published on April 19, 2008
Nucl. Acids Res. 2008 36: W465-W469; doi:10.1093/nar/gkn180 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bas E. Dutilh, Ying He, Maarten L. Hekkelman, and Martijn A. Huynen
Signature, a web server for taxonomic characterization of sequence samples using signature genes
Nucleic Acids Research Advance Access published on May 17, 2008
Nucl. Acids Res. 2008 36: W470-W474; doi:10.1093/nar/gkn277 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Li-Wei Jiang, Kuang-Lun Lin, and Chin Lung Lu
OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes
Nucleic Acids Research Advance Access published on May 2, 2008
Nucl. Acids Res. 2008 36: W475-W480; doi:10.1093/nar/gkn240 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Karsten Suhre and Philippe Schmitt-Kopplin
MassTRIX: mass translator into pathways
Nucleic Acids Research Advance Access published on April 28, 2008
Nucl. Acids Res. 2008 36: W481-W484; doi:10.1093/nar/gkn194 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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
ISPIDER Central: an integrated database web-server for proteomics
Nucleic Acids Research Advance Access published on April 25, 2008
Nucl. Acids Res. 2008 36: W485-W490; doi:10.1093/nar/gkn196 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Seong-Jin Park, Jong-Soon Choi, Seung Il Kim, Jong Bhak, and Sunghoon Lee
MassNet: a functional annotation service for protein mass spectrometry data
Nucleic Acids Research Advance Access published on April 29, 2008
Nucl. Acids Res. 2008 36: W491-W495; doi:10.1093/nar/gkn241 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

David S. Wishart, David Arndt, Mark Berjanskii, Peter Tang, Jianjun Zhou, and Guohui Lin
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: W496-W502; doi:10.1093/nar/gkn305 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Xavier Brochet, Marie-Paule Lefranc, and Véronique Giudicelli
IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis
Nucleic Acids Research Advance Access published on May 24, 2008
Nucl. Acids Res. 2008 36: W503-W508; doi:10.1093/nar/gkn316 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Claus Lundegaard, Kasper Lamberth, Mikkel Harndahl, Søren Buus, Ole Lund, and Morten Nielsen
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11
Nucleic Acids Research Advance Access published on May 7, 2008
Nucl. Acids Res. 2008 36: W509-W512; doi:10.1093/nar/gkn202 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

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
Immune epitope database analysis resource (IEDB-AR)
Nucleic Acids Research Advance Access published on May 31, 2008
Nucl. Acids Res. 2008 36: W513-W518; doi:10.1093/nar/gkn254 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Magdalena Feldhahn, Philipp Thiel, Mathias M. Schuler, Nina Hillen, Stefan Stevanovic, Hans-Georg Rammensee, and Oliver Kohlbacher
EpiToolKit—a web server for computational immunomics
Nucleic Acids Research Advance Access published on April 24, 2008
Nucl. Acids Res. 2008 36: W519-W522; doi:10.1093/nar/gkn229 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

E. Mejía-Roa, P. Carmona-Saez, R. Nogales, C. Vicente, M. Vázquez, X. Y. Yang, C. García, F. Tirado, and A. Pascual-Montano
bioNMF: a web-based tool for nonnegative matrix factorization in biology
Nucleic Acids Research Advance Access published on May 30, 2008
Nucl. Acids Res. 2008 36: W523-W528; doi:10.1093/nar/gkn335 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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