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  		Contents: Volume 37, Web Server issue, 1 July 2009   [Index by Author] 

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Editorial: 2009 Web Server Issue Back

Gary Benson
Nucleic Acids Research annual Web Server Issue in 2009
Nucleic Acids Research Advance Access published on June 4, 2009
Nucl. Acids Res. 2009 37: W1-W2; doi:10.1093/nar/gkp505 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Articles Back

Michelle D. Brazas, Joseph Tadashi Yamada, and B. F. Francis Ouellette
Evolution in bioinformatic resources: 2009 update on the Bioinformatics Links Directory
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: W3-W5; doi:10.1093/nar/gkp531 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Web Server Summaries]  

Hamish Mcwilliam, Franck Valentin, Mickael Goujon, Weizhong Li, Menaka Narayanasamy, Jenny Martin, Teresa Miyar, and Rodrigo Lopez
Web services at the European Bioinformatics Institute-2009
Nucleic Acids Research Advance Access published on May 12, 2009
Nucl. Acids Res. 2009 37: W6-W10; doi:10.1093/nar/gkp302 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yeondae Kwon, Yasumasa Shigemoto, Yoshikazu Kuwana, and Hideaki Sugawara
Web API for biology with a workflow navigation system
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: W11-W16; doi:10.1093/nar/gkp300 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tadashi Imanishi and Hajime Nakaoka
Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases
Nucleic Acids Research Advance Access published on May 19, 2009
Nucl. Acids Res. 2009 37: W17-W22; doi:10.1093/nar/gkp355 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Syed Haider, Benoit Ballester, Damian Smedley, Junjun Zhang, Peter Rice, and Arek Kasprzyk
BioMart Central Portal—unified access to biological data
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W23-W27; doi:10.1093/nar/gkp265 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jeff Elhai, Arnaud Taton, JP Massar, John K. Myers, Mike Travers, Johnny Casey, Mark Slupesky, and Jeff Shrager
BioBIKE: A Web-based, programmable, integrated biological knowledge base
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: W28-W32; doi:10.1093/nar/gkp354 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Xiaoqiao Liu, Jianmin Wu, Jun Wang, Xiaochuan Liu, Shuqi Zhao, Zhe Li, Lei Kong, Xiaocheng Gu, Jingchu Luo, and Ge Gao
WebLab: a data-centric, knowledge-sharing bioinformatic platform
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W33-W39; doi:10.1093/nar/gkp428 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Michael J. Czar, Yizhi Cai, and Jean Peccoud
Writing DNA with GenoCADTM
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W40-W47; doi:10.1093/nar/gkp361 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bernd W. Brandt and Jaap Heringa
webPRC: the Profile Comparer for alignment-based searching of public domain databases
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W48-W52; doi:10.1093/nar/gkp279 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marianne M. Lee, Michael K. Chan, and Ralf Bundschuh
SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W53-W56; doi:10.1093/nar/gkp301 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Akihiro Matsushima, Norio Kobayashi, Yoshiki Mochizuki, Manabu Ishii, Shuji Kawaguchi, Takaho A. Endo, Ryo Umetsu, Yuko Makita, and Tetsuro Toyoda
OmicBrowse: a Flash-based high-performance graphics interface for genomic resources
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: W57-W62; doi:10.1093/nar/gkp404 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fiona Achcar, Jean-Michel Camadro, and Denis Mestivier
AutoClass@IJM: a powerful tool for Bayesian classification of heterogeneous data in biology
Nucleic Acids Research Advance Access published on May 27, 2009
Nucl. Acids Res. 2009 37: W63-W67; doi:10.1093/nar/gkp430 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Michael Hackenberg, Martin Sturm, David Langenberger, Juan Manuel Falcón-Pérez, and Ana M. Aransay
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: W68-W76; doi:10.1093/nar/gkp347 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Chun Liang, Lin Liu, and Guoli Ji
WebGMAP: a web service for mapping and aligning cDNA sequences to genomes
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W77-W83; doi:10.1093/nar/gkp389 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, and Kimmen Sjölander
Berkeley PHOG: PhyloFacts orthology group prediction web server
Nucleic Acids Research Advance Access published on May 12, 2009
Nucl. Acids Res. 2009 37: W84-W89; doi:10.1093/nar/gkp373 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Ruslan I. Sadreyev, Ming Tang, Bong-Hyun Kim, and Nick V. Grishin
COMPASS server for homology detection: improved statistical accuracy, speed and functionality
Nucleic Acids Research Advance Access published on May 12, 2009
Nucl. Acids Res. 2009 37: W90-W94; doi:10.1093/nar/gkp360 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bruno Contreras-Moreira, Bernardo Sachman-Ruiz, Iraís Figueroa-Palacios, and Pablo Vinuesa
primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies
Nucleic Acids Research Advance Access published on May 21, 2009
Nucl. Acids Res. 2009 37: W95-W100; doi:10.1093/nar/gkp377 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Katharina J. Hoff, Thomas Lingner, Peter Meinicke, and Maike Tech
Orphelia: predicting genes in metagenomic sequencing reads
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W101-W105; doi:10.1093/nar/gkp327 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, and Roded Sharan
Torque: topology-free querying of protein interaction networks
Nucleic Acids Research Advance Access published on June 2, 2009
Nucl. Acids Res. 2009 37: W106-W108; doi:10.1093/nar/gkp474 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Pablo Minguez, Stefan Götz, David Montaner, Fatima Al-Shahrour, and Joaquin Dopazo
SNOW, a web-based tool for the statistical analysis of protein–protein interaction networks
Nucleic Acids Research Advance Access published on May 19, 2009
Nucl. Acids Res. 2009 37: W109-W114; doi:10.1093/nar/gkp402 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zhenjun Hu, Jui-Hung Hung, Yan Wang, Yi-Chien Chang, Chia-Ling Huang, Matt Huyck, and Charles DeLisi
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
Nucleic Acids Research Advance Access published on May 21, 2009
Nucl. Acids Res. 2009 37: W115-W121; doi:10.1093/nar/gkp406 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Hagen Blankenburg, Fidel Ramírez, Joachim Büch, and Mario Albrecht
DASMIweb: online integration, analysis and assessment of distributed protein interaction data
Nucleic Acids Research Advance Access published on June 5, 2009
Nucl. Acids Res. 2009 37: W122-W128; doi:10.1093/nar/gkp438 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chih-Hung Chou, Wen-Chi Chang, Chih-Min Chiu, Chih-Chang Huang, and Hsien-Da Huang
FMM: a web server for metabolic pathway reconstruction and comparative analysis
Nucleic Acids Research Advance Access published on April 28, 2009
Nucl. Acids Res. 2009 37: W129-W134; doi:10.1093/nar/gkp264 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Matthias Frisch, Bernward Klocke, Manuela Haltmeier, and Kornelie Frech
LitInspector: literature and signal transduction pathway mining in PubMed abstracts
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: W135-W140; doi:10.1093/nar/gkp303 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jean-Fred Fontaine, Adriano Barbosa-Silva, Martin Schaefer, Matthew R. Huska, Enrique M. Muro, and Miguel A. Andrade-Navarro
MedlineRanker: flexible ranking of biomedical literature
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W141-W146; doi:10.1093/nar/gkp353 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Yuko Yoshida, Yuko Makita, Naohiko Heida, Satomi Asano, Akihiro Matsushima, Manabu Ishii, Yoshiki Mochizuki, Hiroshi Masuya, Shigeharu Wakana, Norio Kobayashi, and Tetsuro Toyoda
PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning
Nucleic Acids Research Advance Access published on May 25, 2009
Nucl. Acids Res. 2009 37: W147-W152; doi:10.1093/nar/gkp384 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Miguel Vazquez, Pedro Carmona-Saez, Ruben Nogales-Cadenas, Monica Chagoyen, Francisco Tirado, Jose Maria Carazo, and Alberto Pascual-Montano
SENT: semantic features in text
Nucleic Acids Research Advance Access published on May 20, 2009
Nucl. Acids Res. 2009 37: W153-W159; doi:10.1093/nar/gkp392 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Martin Krallinger, Carlos Rodriguez-Penagos, Ashish Tendulkar, and Alfonso Valencia
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction
Nucleic Acids Research Advance Access published on June 11, 2009
Nucl. Acids Res. 2009 37: W160-W165; doi:10.1093/nar/gkp484 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, and Toshihisa Takagi
Gendoo: Functional profiling of gene and disease features using MeSH vocabulary
Nucleic Acids Research Advance Access published on June 4, 2009
Nucl. Acids Res. 2009 37: W166-W169; doi:10.1093/nar/gkp483 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Natalya F. Noy, Nigam H. Shah, Patricia L. Whetzel, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Daniel L. Rubin, Margaret-Anne Storey, Christopher G. Chute, and Mark A. Musen
BioPortal: ontologies and integrated data resources at the click of a mouse
Nucleic Acids Research Advance Access published on May 29, 2009
Nucl. Acids Res. 2009 37: W170-W173; doi:10.1093/nar/gkp440 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Zhao Xu and Bailin Hao
CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes
Nucleic Acids Research Advance Access published on April 26, 2009
Nucl. Acids Res. 2009 37: W174-W178; doi:10.1093/nar/gkp278 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jorn Bruggeman, Jaap Heringa, and Bernd W. Brandt
PhyloPars: estimation of missing parameter values using phylogeny
Nucleic Acids Research Advance Access published on May 13, 2009
Nucl. Acids Res. 2009 37: W179-W184; doi:10.1093/nar/gkp370 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Fabian Schreiber, Gert Wörheide, and Burkhard Morgenstern
OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences
Nucleic Acids Research Advance Access published on June 2, 2009
Nucl. Acids Res. 2009 37: W185-W188; doi:10.1093/nar/gkp434 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Schraga Schwartz, Eitan Hall, and Gil Ast
SROOGLE: webserver for integrative, user-friendly visualization of splicing signals
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W189-W192; doi:10.1093/nar/gkp320 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Deepak Sharma, Debasisa Mohanty, and Avadhesha Surolia
RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways
Nucleic Acids Research Advance Access published on May 21, 2009
Nucl. Acids Res. 2009 37: W193-W201; doi:10.1093/nar/gkp388 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Timothy L. Bailey, Mikael Boden, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, and William S. Noble
MEME SUITE: tools for motif discovery and searching
Nucleic Acids Research Advance Access published on May 20, 2009
Nucl. Acids Res. 2009 37: W202-W208; doi:10.1093/nar/gkp335 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Robin Boutros, Nicola Stokes, Michaël Bekaert, and Emma C. Teeling
UniPrime2: a web service providing easier Universal Primer design
Nucleic Acids Research Advance Access published on April 28, 2009
Nucl. Acids Res. 2009 37: W209-W213; doi:10.1093/nar/gkp269 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Marcus Bode, Samuel Khor, Hongye Ye, Mo-Huang Li, and Jackie Y. Ying
TmPrime: fast, flexible oligonucleotide design software for gene synthesis
Nucleic Acids Research Advance Access published on June 10, 2009
Nucl. Acids Res. 2009 37: W214-W221; doi:10.1093/nar/gkp461 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Richard Boyce, Parmit Chilana, and Timothy M. Rose
iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences
Nucleic Acids Research Advance Access published on May 14, 2009
Nucl. Acids Res. 2009 37: W222-W228; doi:10.1093/nar/gkp379 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Adam M. Phillippy, Kunmi Ayanbule, Nathan J. Edwards, and Steven L. Salzberg
Insignia: a DNA signature search web server for diagnostic assay development
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: W229-W234; doi:10.1093/nar/gkp286 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marc van Dijk and Alexandre M. J. J. Bonvin
3D-DART: a DNA structure modelling server
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: W235-W239; doi:10.1093/nar/gkp287 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Guohui Zheng, Xiang-Jun Lu, and Wilma K. Olson
Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures
Nucleic Acids Research Advance Access published on May 27, 2009
Nucl. Acids Res. 2009 37: W240-W246; doi:10.1093/nar/gkp358 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Federico Zambelli, Graziano Pesole, and Giulio Pavesi
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
Nucleic Acids Research Advance Access published on May 31, 2009
Nucl. Acids Res. 2009 37: W247-W252; doi:10.1093/nar/gkp464 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jeffrey P. Mower
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: W253-W259; doi:10.1093/nar/gkp337 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Emidio Capriotti and Marc A. Marti-Renom
SARA: a server for function annotation of RNA structures
Nucleic Acids Research Advance Access published on May 29, 2009
Nucl. Acids Res. 2009 37: W260-W265; doi:10.1093/nar/gkp433 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jean Hausser, Philipp Berninger, Christoph Rodak, Yvonne Jantscher, Stefan Wirth, and Mihaela Zavolan
MirZ: an integrated microRNA expression atlas and target prediction resource
Nucleic Acids Research Advance Access published on May 25, 2009
Nucl. Acids Res. 2009 37: W266-W272; doi:10.1093/nar/gkp412 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

M. Maragkakis, M. Reczko, V. A. Simossis, P. Alexiou, G. L. Papadopoulos, T. Dalamagas, G. Giannopoulos, G. Goumas, E. Koukis, K. Kourtis, T. Vergoulis, N. Koziris, T. Sellis, P. Tsanakas, and A. G. Hatzigeorgiou
DIANA-microT web server: elucidating microRNA functions through target prediction
Nucleic Acids Research Advance Access published on April 30, 2009
Nucl. Acids Res. 2009 37: W273-W276; doi:10.1093/nar/gkp292 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kengo Sato, Michiaki Hamada, Kiyoshi Asai, and Toutai Mituyama
CENTROIDFOLD: a web server for RNA secondary structure prediction
Nucleic Acids Research Advance Access published on May 12, 2009
Nucl. Acids Res. 2009 37: W277-W280; doi:10.1093/nar/gkp367 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jerome Waldispühl, Srinivas Devadas, Bonnie Berger, and Peter Clote
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
Nucleic Acids Research Advance Access published on June 16, 2009
Nucl. Acids Res. 2009 37: W281-W286; doi:10.1093/nar/gkp477 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chin-En Lai, Ming-Yuan Tsai, Yun-Chen Liu, Chih-Wei Wang, Kun-Tze Chen, and Chin Lung Lu
FASTR3D: a fast and accurate search tool for similar RNA 3D structures
Nucleic Acids Research Advance Access published on May 12, 2009
Nucl. Acids Res. 2009 37: W287-W295; doi:10.1093/nar/gkp330 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexandre Gattiker, Christophe Dessimoz, Adrian Schneider, Ioannis Xenarios, Marco Pagni, and Jacques Rougemont
The Microbe browser for comparative genomics
Nucleic Acids Research Advance Access published on April 30, 2009
Nucl. Acids Res. 2009 37: W296-W299; doi:10.1093/nar/gkp268 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Conrad Plake, Loic Royer, Rainer Winnenburg, Jörg Hakenberg, and Michael Schroeder
GoGene: gene annotation in the fast lane
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W300-W304; doi:10.1093/nar/gkp429 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jing Chen, Eric E. Bardes, Bruce J. Aronow, and Anil G. Jegga
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W305-W311; doi:10.1093/nar/gkp427 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gabriele Schweikert, Jonas Behr, Alexander Zien, Georg Zeller, Cheng Soon Ong, Sören Sonnenburg, and Gunnar Rätsch
mGene.web: a web service for accurate computational gene finding
Nucleic Acids Research Advance Access published on June 3, 2009
Nucl. Acids Res. 2009 37: W312-W316; doi:10.1093/nar/gkp479 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ruben Nogales-Cadenas, Pedro Carmona-Saez, Miguel Vazquez, Cesar Vicente, Xiaoyuan Yang, Francisco Tirado, Jose María Carazo, and Alberto Pascual-Montano
GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W317-W322; doi:10.1093/nar/gkp416 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexey V. Antonov, Sabine Dietmann, Philip Wong, Dominik Lutter, and Hans W. Mewes
GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W323-W328; doi:10.1093/nar/gkp313 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Daniel Glez-Peña, Gonzalo Gómez-López, David G. Pisano, and Florentino Fdez-Riverola
WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis
Nucleic Acids Research Advance Access published on April 30, 2009
Nucl. Acids Res. 2009 37: W329-W334; doi:10.1093/nar/gkp263 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Nicolas Goffard, Tancred Frickey, and Georg Weiller
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways
Nucleic Acids Research Advance Access published on May 27, 2009
Nucl. Acids Res. 2009 37: W335-W339; doi:10.1093/nar/gkp432 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ignacio Medina, David Montaner, Nuria Bonifaci, Miguel Angel Pujana, José Carbonell, Joaquin Tarraga, Fatima Al-Shahrour, and Joaquin Dopazo
Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies
Nucleic Acids Research Advance Access published on June 5, 2009
Nucl. Acids Res. 2009 37: W340-W344; doi:10.1093/nar/gkp481 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Zhidian Du, Lin Li, Chin-Fu Chen, Philip S. Yu, and James Z. Wang
G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery
Nucleic Acids Research Advance Access published on June 2, 2009
Nucl. Acids Res. 2009 37: W345-W349; doi:10.1093/nar/gkp463 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Choong-Hyun Sun, Min-Sung Kim, Youngwoong Han, and Gwan-Su Yi
COFECO: composite function annotation enriched by protein complex data
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W350-W355; doi:10.1093/nar/gkp331 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Seungyoon Nam, Meng Li, Kwangmin Choi, Curtis Balch, Sun Kim, and Kenneth P. Nephew
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W356-W362; doi:10.1093/nar/gkp294 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Guy Naamati, Manor Askenazi, and Michal Linial
ClanTox: a classifier of short animal toxins
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W363-W368; doi:10.1093/nar/gkp299 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chun-Chen Chen, Chun-Yu Lin, Yu-Shu Lo, and Jinn-Moon Yang
PPISearch: a web server for searching homologous protein–protein interactions across multiple species
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: W369-W375; doi:10.1093/nar/gkp309 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Antonin Pavelka, Eva Chovancova, and Jiri Damborsky
HotSpot Wizard: a web server for identification of hot spots in protein engineering
Nucleic Acids Research Advance Access published on May 21, 2009
Nucl. Acids Res. 2009 37: W376-W383; doi:10.1093/nar/gkp410 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yan Yuan Tseng, Craig Dupree, Z. Jeffrey Chen, and Wen-Hsiung Li
SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns
Nucleic Acids Research Advance Access published on April 30, 2009
Nucl. Acids Res. 2009 37: W384-W389; doi:10.1093/nar/gkp308 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sriram Sankararaman, Bryan Kolaczkowski, and Kimmen Sjölander
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
Nucleic Acids Research Advance Access published on May 13, 2009
Nucl. Acids Res. 2009 37: W390-W395; doi:10.1093/nar/gkp339 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Wen-Yi Chu, Yu-Feng Huang, Chun-Chin Huang, Yi-Sheng Cheng, Chien-Kang Huang, and Yen-Jen Oyang
ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors
Nucleic Acids Research Advance Access published on May 29, 2009
Nucl. Acids Res. 2009 37: W396-W401; doi:10.1093/nar/gkp449 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Wijnand T. M. Mooij, Eirini Mitsiki, and Anastassis Perrakis
ProteinCCD: enabling the design of protein truncation constructs for expression and crystallization experiments
Nucleic Acids Research Advance Access published on April 24, 2009
Nucl. Acids Res. 2009 37: W402-W405; doi:10.1093/nar/gkp256 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lun Yang, Heng Luo, Jian Chen, Qinghe Xing, and Lin He
SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical–protein interactome
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: W406-W412; doi:10.1093/nar/gkp312 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Marylens Hernandez, Dario Ghersi, and Roberto Sanchez
SITEHOUND-web: a server for ligand binding site identification in protein structures
Nucleic Acids Research Advance Access published on April 26, 2009
Nucl. Acids Res. 2009 37: W413-W416; doi:10.1093/nar/gkp281 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Duangdao Wichadakul, Somrak Numnark, and Supawadee Ingsriswang
d-Omix: a mixer of generic protein domain analysis tools
Nucleic Acids Research Advance Access published on May 21, 2009
Nucl. Acids Res. 2009 37: W417-W421; doi:10.1093/nar/gkp329 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexander A. Kantardjiev and Boris P. Atanasov
PHEMTO: protein pH-dependent electric moment tools
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W422-W427; doi:10.1093/nar/gkp336 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Arnold Kuzniar, Ke Lin, Ying He, Harm Nijveen, Sándor Pongor, and Jack A. M. Leunissen
ProGMap: an integrated annotation resource for protein orthology
Nucleic Acids Research Advance Access published on June 3, 2009
Nucl. Acids Res. 2009 37: W428-W434; doi:10.1093/nar/gkp462 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hong Sain Ooi, Chia Yee Kwo, Michael Wildpaner, Fernanda L. Sirota, Birgit Eisenhaber, Sebastian Maurer-Stroh, Wing Cheong Wong, Alexander Schleiffer, Frank Eisenhaber, and Georg Schneider
ANNIE: integrated de novo protein sequence annotation
Nucleic Acids Research Advance Access published on April 23, 2009
Nucl. Acids Res. 2009 37: W435-W440; doi:10.1093/nar/gkp254 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

R. Z. Cer, U. Mudunuri, R. Stephens, and F. J. Lebeda
IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding
Nucleic Acids Research Advance Access published on April 24, 2009
Nucl. Acids Res. 2009 37: W441-W445; doi:10.1093/nar/gkp253 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Michael Remmert, Dirk Linke, Andrei N. Lupas, and Johannes Söding
HHomp—prediction and classification of outer membrane proteins
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W446-W451; doi:10.1093/nar/gkp325 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Smriti Shridhar, Debasis Chattopadhyay, and Gitanjali Yadav
PLecDom: a program for identification and analysis of plant lectin domains
Nucleic Acids Research Advance Access published on May 27, 2009
Nucl. Acids Res. 2009 37: W452-W458; doi:10.1093/nar/gkp409 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Gaëlle Debret, Arnaud Martel, and Philippe Cuniasse
RASMOT-3D PRO: a 3D motif search webserver
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: W459-W464; doi:10.1093/nar/gkp304 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Andreas Bernsel, Håkan Viklund, Aron Hennerdal, and Arne Elofsson
TOPCONS: consensus prediction of membrane protein topology
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W465-W468; doi:10.1093/nar/gkp363 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Changsik Kim, Jiwon Choi, Seong Joon Lee, William J. Welsh, and Sukjoon Yoon
NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation
Nucleic Acids Research Advance Access published on May 25, 2009
Nucl. Acids Res. 2009 37: W469-W473; doi:10.1093/nar/gkp351 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Aroop Sircar, Eric T. Kim, and Jeffrey J. Gray
RosettaAntibody: antibody variable region homology modeling server
Nucleic Acids Research Advance Access published on May 20, 2009
Nucl. Acids Res. 2009 37: W474-W479; doi:10.1093/nar/gkp387 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Thomas Margraf, Gundolf Schenk, and Andrew E. Torda
The SALAMI protein structure search server
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W480-W484; doi:10.1093/nar/gkp431 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jean-Luc Pons and Gilles Labesse
@TOME-2: a new pipeline for comparative modeling of protein–ligand complexes
Nucleic Acids Research Advance Access published on May 13, 2009
Nucl. Acids Res. 2009 37: W485-W491; doi:10.1093/nar/gkp368 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kevin Karplus
SAM-T08, HMM-based protein structure prediction
Nucleic Acids Research Advance Access published on May 29, 2009
Nucl. Acids Res. 2009 37: W492-W497; doi:10.1093/nar/gkp403 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Julien Maupetit, Philippe Derreumaux, and Pierre Tuffery
PEP-FOLD: an online resource for de novo peptide structure prediction
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: W498-W503; doi:10.1093/nar/gkp323 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

O. Sperandio, M. Petitjean, and P. Tuffery
wwLigCSRre: a 3D ligand-based server for hit identification and optimization
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W504-W509; doi:10.1093/nar/gkp324 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Pascal Benkert, Michael Künzli, and Torsten Schwede
QMEAN server for protein model quality estimation
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W510-W514; doi:10.1093/nar/gkp322 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Allison N. Tegge, Zheng Wang, Jesse Eickholt, and Jianlin Cheng
NNcon: improved protein contact map prediction using 2D-recursive neural networks
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W515-W518; doi:10.1093/nar/gkp305 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Weerayuth Kittichotirat, Michal Guerquin, Roger E. Bumgarner, and Ram Samudrala
Protinfo PPC: A web server for atomic level prediction of protein complexes
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W519-W525; doi:10.1093/nar/gkp306 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Shuoyong Shi, Bhadrachalam Chitturi, and Nick V. Grishin
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W526-W531; doi:10.1093/nar/gkp316 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Bong-Hyun Kim, Hua Cheng, and Nick V. Grishin
HorA web server to infer homology between proteins using sequence and structural similarity
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: W532-W538; doi:10.1093/nar/gkp328 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Stefan J. Suhrer, Markus Wiederstein, Markus Gruber, and Manfred J. Sippl
COPS—a novel workbench for explorations in fold space
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W539-W544; doi:10.1093/nar/gkp411 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Wei-Cheng Lo, Che-Yu Lee, Chi-Ching Lee, and Ping-Chiang Lyu
iSARST: an integrated SARST web server for rapid protein structural similarity searches
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W545-W551; doi:10.1093/nar/gkp291 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Darby Tien-Hao Chang, Ting-Ying Chien, and Chien-Yu Chen
seeMotif: exploring and visualizing sequence motifs in 3D structures
Nucleic Acids Research Advance Access published on May 28, 2009
Nucl. Acids Res. 2009 37: W552-W558; doi:10.1093/nar/gkp439 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Po-Hsien Lee, Kuei-Ling Kuo, Pei-Ying Chu, Eric M. Liu, and Jung-Hsin Lin
SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters
Nucleic Acids Research Advance Access published on May 11, 2009
Nucl. Acids Res. 2009 37: W559-W564; doi:10.1093/nar/gkp359 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Stefano Angaran, Mary Ellen Bock, Claudio Garutti, and Concettina Guerra
MolLoc: a web tool for the local structural alignment of molecular surfaces
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W565-W570; doi:10.1093/nar/gkp405 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Peter W. Hildebrand, Andrean Goede, Raphael A. Bauer, Bjoern Gruening, Jochen Ismer, Elke Michalsky, and Robert Preissner
SuperLooper—a prediction server for the modeling of loops in globular and membrane proteins
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W571-W574; doi:10.1093/nar/gkp338 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexander Rose, Stephan Lorenzen, Andrean Goede, Björn Gruening, and Peter W. Hildebrand
RHYTHM—a server to predict the orientation of transmembrane helices in channels and membrane-coils
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W575-W580; doi:10.1093/nar/gkp418 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Edward R. Morrissey and Ramón Diaz-Uriarte
Pomelo II: finding differentially expressed genes
Nucleic Acids Research Advance Access published on May 12, 2009
Nucl. Acids Res. 2009 37: W581-W586; doi:10.1093/nar/gkp366 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Darya Krushevskaya, Hedi Peterson, Jüri Reimand, Meelis Kull, and Jaak Vilo
VisHiC—hierarchical functional enrichment analysis of microarray data
Nucleic Acids Research Advance Access published on May 29, 2009
Nucl. Acids Res. 2009 37: W587-W592; doi:10.1093/nar/gkp435 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Dominik Seelow, Markus Schuelke, Friedhelm Hildebrandt, and Peter Nürnberg
HomozygosityMapper—an interactive approach to homozygosity mapping
Nucleic Acids Research Advance Access published on May 21, 2009
Nucl. Acids Res. 2009 37: W593-W599; doi:10.1093/nar/gkp369 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Zongli Xu and Jack A. Taylor
SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies
Nucleic Acids Research Advance Access published on May 5, 2009
Nucl. Acids Res. 2009 37: W600-W605; doi:10.1093/nar/gkp290 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Lee S. Katz, Chris R. Bolen, Brian H. Harcourt, Susanna Schmink, Xin Wang, Andrey Kislyuk, Robert T. Taylor, Leonard W. Mayer, and I. King Jordan
Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data
Nucleic Acids Research Advance Access published on May 25, 2009
Nucl. Acids Res. 2009 37: W606-W611; doi:10.1093/nar/gkp288 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Jing Sun, Di Wu, Tianlei Xu, Xiaojing Wang, Xiaolian Xu, Lin Tao, Y. X. Li, and Z. W. Cao
SEPPA: a computational server for spatial epitope prediction of protein antigens
Nucleic Acids Research Advance Access published on May 22, 2009
Nucl. Acids Res. 2009 37: W612-W616; doi:10.1093/nar/gkp417 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Nora C. Toussaint and Oliver Kohlbacher
OptiTope—a web server for the selection of an optimal set of peptides for epitope-based vaccines
Nucleic Acids Research Advance Access published on May 6, 2009
Nucl. Acids Res. 2009 37: W617-W622; doi:10.1093/nar/gkp293 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yanli Wang, Jewen Xiao, Tugba O. Suzek, Jian Zhang, Jiyao Wang, and Stephen H. Bryant
PubChem: a public information system for analyzing bioactivities of small molecules
Nucleic Acids Research Advance Access published on June 4, 2009
Nucl. Acids Res. 2009 37: W623-W633; doi:10.1093/nar/gkp456 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Luiz Carlos Junior Alcantara, Sharon Cassol, Pieter Libin, Koen Deforche, Oliver G. Pybus, Marc Van Ranst, Bernardo Galvão-Castro, Anne-Mieke Vandamme, and Tulio de Oliveira
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
Nucleic Acids Research Advance Access published on May 29, 2009
Nucl. Acids Res. 2009 37: W634-W642; doi:10.1093/nar/gkp455 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yu-Chieh Liao, Chin-Yu Ko, Ming-Hsin Tsai, Min-Shi Lee, and Chao A. Hsiung
ATIVS: analytical tool for influenza virus surveillance
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W643-W646; doi:10.1093/nar/gkp321 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Anne-Kathrin Schultz, Ming Zhang, Ingo Bulla, Thomas Leitner, Bette Korber, Burkhard Morgenstern, and Mario Stanke
jpHMM: Improving the reliability of recombination prediction in HIV-1
Nucleic Acids Research Advance Access published on May 14, 2009
Nucl. Acids Res. 2009 37: W647-W651; doi:10.1093/nar/gkp371 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jianguo Xia, Nick Psychogios, Nelson Young, and David S. Wishart
MetaboAnalyst: a web server for metabolomic data analysis and interpretation
Nucleic Acids Research Advance Access published on May 8, 2009
Nucl. Acids Res. 2009 37: W652-W660; doi:10.1093/nar/gkp356 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chih-Chiang Tsou, Yin-Hao Tsui, Yi-Hwa Yian, Yi-Ju Chen, Han-Yin Yang, Chuan-Yih Yu, Ke-Shiuan Lynn, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC–MS
Nucleic Acids Research Advance Access published on June 15, 2009
Nucl. Acids Res. 2009 37: W661-W669; doi:10.1093/nar/gkp476 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Mark Berjanskii, Peter Tang, Jack Liang, Joseph A. Cruz, Jianjun Zhou, You Zhou, Edward Bassett, Cam MacDonell, Paul Lu, Guohui Lin, and David S. Wishart
GeNMR: a web server for rapid NMR-based protein structure determination
Nucleic Acids Research Advance Access published on April 30, 2009
Nucl. Acids Res. 2009 37: W670-W677; doi:10.1093/nar/gkp280 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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Nucleic Acids Research: VOLUME 37 WEB SERVER ISSUE JULY 1, 2009
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