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  		Contents: Volume 35, Web Server issue, July 2007   [Index by Author]  [Cover Caption] 

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Editorials Back

Gary Benson
Editorial
Nucl. Acids Res. 2007 35: W1; doi:10.1093/nar/gkm484 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Articles Back

Joanne A. Fox, Scott McMillan, and B. F. Francis Ouellette
Conducting Research on the Web: 2007 Update for the Bioinformatics Links Directory
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: W3-W5; doi:10.1093/nar/gkm459 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Web Server Summaries]  

Alberto Labarga, Franck Valentin, Mikael Anderson, and Rodrigo Lopez
Web Services at the European Bioinformatics Institute
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: W6-W11; doi:10.1093/nar/gkm291 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mounir Errami, Jonathan D. Wren, Justin M. Hicks, and Harold R. Garner
eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: W12-W15; doi:10.1093/nar/gkm221 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ildefonso Cases, David G. Pisano, Eduardo Andres, Angel Carro, José M. Fernández, Gonzalo Gómez-López, Jose M. Rodriguez, Jaime F. Vera, Alfonso Valencia, and Ana M. Rojas
CARGO: a web portal to integrate customized biological information
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: W16-W20; doi:10.1093/nar/gkm280 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

José M. Fernández, Robert Hoffmann, and Alfonso Valencia
iHOP web services
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W21-W26; doi:10.1093/nar/gkm298 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy, and Kimmen Sjölander
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W27-W32; doi:10.1093/nar/gkm325 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Thomas M. Keane, Thomas J. Naughton, and James O. McInerney
MultiPhyl: a high-throughput phylogenomics webserver using distributed computing
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: W33-W37; doi:10.1093/nar/gkm359 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Joaquín Tárraga, Ignacio Medina, Leonardo Arbiza, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, and Hernán Dopazo
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: W38-W42; doi:10.1093/nar/gkm224 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Warren A. Kibbe
OligoCalc: an online oligonucleotide properties calculator
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: W43-W46; doi:10.1093/nar/gkm234 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Peng Jiang, Haonan Wu, Jiawei Wei, Fei Sang, Xiao Sun, and Zuhong Lu
RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W47-W51; doi:10.1093/nar/gkm217 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ibtissem Grissa, Gilles Vergnaud, and Christine Pourcel
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W52-W57; doi:10.1093/nar/gkm360 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Roy Eric Collins and Gabrielle Rocap
REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis
Nucl. Acids Res. 2007 35: W58-W62; doi:10.1093/nar/gkm384 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ming-Fang Tsai, Yi-Jung Lin, Yu-Chang Cheng, Kuo-Hsi Lee, Cheng-Chih Huang, Yuan-Tsong Chen, and Adam Yao
PrimerZ: streamlined primer design for promoters, exons and human SNPs
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W63-W65; doi:10.1093/nar/gkm383 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yung-Fu Chen, Rung-Ching Chen, Lin-Yu Tseng, Elong Lin, Yung-Kuan Chan, and Ren-Hao Pan
NTMG (N-terminal Truncated Mutants Generator for cDNA): an automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W66-W70; doi:10.1093/nar/gkm305 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andreas Untergasser, Harm Nijveen, Xiangyu Rao, Ton Bisseling, René Geurts, and Jack A.M. Leunissen
Primer3Plus, an enhanced web interface to Primer3
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W71-W74; doi:10.1093/nar/gkm306 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ramón Díaz-Uriarte, Andreu Alibés, Edward R. Morrissey, Andrés Cañada, Oscar M. Rueda, and Mariana L. Neves
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W75-W80; doi:10.1093/nar/gkm229 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lucía Conde, David Montaner, Jordi Burguet-Castell, Joaquín Tárraga, Ignacio Medina, Fátima Al-Shahrour, and Joaquín Dopazo
ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling
Nucleic Acids Research Advance Access published on April 27, 2007
Nucl. Acids Res. 2007 35: W81-W85; doi:10.1093/nar/gkm257 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hubert Rehrauer, Stefan Zoller, and Ralph Schlapbach
MAGMA: analysis of two-channel microarrays made easy
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W86-W90; doi:10.1093/nar/gkm302 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, Ignacio Medina, Eva Alloza, David Montaner, and Joaquín Dopazo
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W91-W96; doi:10.1093/nar/gkm260 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Hong-Yu Ou, Xinyi He, Ewan M. Harrison, Bridget R. Kulasekara, Ali Bin Thani, Aras Kadioglu, Stephen Lory, Jay C. D. Hinton, Michael R. Barer, Zixin Deng, and Kumar Rajakumar
MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W97-W104; doi:10.1093/nar/gkm380 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yue Lu, Xin He, and Sheng Zhong
Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease
Nucleic Acids Research Advance Access published on June 1, 2007
Nucl. Acids Res. 2007 35: W105-W114; doi:10.1093/nar/gkm408 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Deepak Grover, Alonzo S. Woodfield, Ranjana Verma, Peter P. Zandi, Douglas F. Levinson, and James B. Potash
QuickSNP: an automated web server for selection of tagSNPs
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W115-W120; doi:10.1093/nar/gkm329 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hongkun Zheng, Junjie Shi, Xiaodong Fang, Yuan Li, Søren Vang, Wei Fan, Junyi Wang, Zhang Zhang, Wen Wang, Karsten Kristiansen, and Jun Wang
FGF: A web tool for Fishing Gene Family in a whole genome database
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W121-W125; doi:10.1093/nar/gkm426 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Pere Puigbò, Eduard Guzmán, Antoni Romeu, and Santiago Garcia-Vallvé
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: W126-W131; doi:10.1093/nar/gkm219 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Michael C. Angellotti, Shafquat B. Bhuiyan, Guorong Chen, and Xiu-Feng Wan
CodonO: codon usage bias analysis within and across genomes
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W132-W136; doi:10.1093/nar/gkm392 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chun Liang, Gang Wang, Lin Liu, Guoli Ji, Yuansheng Liu, Jinqiao Chen, Jason S. Webb, Greg Reese, and Jeffrey F. D. Dean
WebTraceMiner: a web service for processing and mining EST sequence trace files
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W137-W142; doi:10.1093/nar/gkm299 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shivashankar H. Nagaraj, Nandan Deshpande, Robin B. Gasser, and Shoba Ranganathan
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform
Nucleic Acids Research Advance Access published on June 1, 2007
Nucl. Acids Res. 2007 35: W143-W147; doi:10.1093/nar/gkm378 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Rowan A. C. Mitchell, Nathalie Castells-Brooke, Jan Taubert, Paul J. Verrier, David J. Leader, and Christopher J. Rawlings
Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence
Nucleic Acids Research Advance Access published on April 16, 2007
Nucl. Acids Res. 2007 35: W148-W151; doi:10.1093/nar/gkm220 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Yan Zhang, Shiuh-Ming Luoh, Lawrence S. Hon, Robert Baertsch, William I. Wood, and Zemin Zhang
GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database
Nucleic Acids Research Advance Access published on June 1, 2007
Nucl. Acids Res. 2007 35: W152-W158; doi:10.1093/nar/gkm381 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Byungwook Lee, Taehui Hong, Sang Jin Byun, Taeha Woo, and Yoon Jeong Choi
ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W159-W162; doi:10.1093/nar/gkm369 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Tomás Norambuena, Rodrigo Malig, and Francisco Melo
SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation
Nucleic Acids Research Advance Access published on July 10, 2007
Nucl. Acids Res. 2007 35: W163-W168; doi:10.1093/nar/gkm429 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Da Wei Huang, Brad T. Sherman, Qina Tan, Joseph Kir, David Liu, David Bryant, Yongjian Guo, Robert Stephens, Michael W. Baseler, H. Clifford Lane, and Richard A. Lempicki
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: W169-W175; doi:10.1093/nar/gkm415 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Nicolas Goffard and Georg Weiller
PathExpress: a web-based tool to identify relevant pathways in gene expression data
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: W176-W181; doi:10.1093/nar/gkm261 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yuki Moriya, Masumi Itoh, Shujiro Okuda, Akiyasu C. Yoshizawa, and Minoru Kanehisa
KAAS: an automatic genome annotation and pathway reconstruction server
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W182-W185; doi:10.1093/nar/gkm321 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Christina Backes, Andreas Keller, Jan Kuentzer, Benny Kneissl, Nicole Comtesse, Yasser A. Elnakady, Rolf Müller, Eckart Meese, and Hans-Peter Lenhof
GeneTrail—advanced gene set enrichment analysis
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W186-W192; doi:10.1093/nar/gkm323 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen, and Jaak Vilo
g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W193-W200; doi:10.1093/nar/gkm226 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Christoph D. Schmid, Thierry Sengstag, Philipp Bucher, and Mauro Delorenzi
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W201-W205; doi:10.1093/nar/gkm343 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Purvesh Khatri, Calin Voichita, Khalid Kattan, Nadeem Ansari, Avani Khatri, Constantin Georgescu, Adi L. Tarca, and Sorin Draghici
Onto-Tools: new additions and improvements in 2006
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W206-W211; doi:10.1093/nar/gkm327 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Carolina Perez-Iratxeta, Peer Bork, and Miguel A. Andrade-Navarro
Update of the G2D tool for prioritization of gene candidates to inherited diseases
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W212-W216; doi:10.1093/nar/gkm223 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Katherine A. Romer, Guy-Richard Kayombya, and Ernest Fraenkel
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W217-W220; doi:10.1093/nar/gkm376 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Huai-Kuang Tsai, Meng-Yuan Chou, Ching-Hua Shih, Grace Tzu-Wei Huang, Tien-Hsien Chang, and Wen-Hsiung Li
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W221-W226; doi:10.1093/nar/gkm379 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, and Kenta Nakai
Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W227-W231; doi:10.1093/nar/gkm362 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

William A. Thompson, Lee A. Newberg, Sean Conlan, Lee Ann McCue, and Charles E. Lawrence
The Gibbs Centroid Sampler
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: W232-W237; doi:10.1093/nar/gkm265 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Li-Wei Chang, Burr R. Fontaine, Gary D. Stormo, and Rakesh Nagarajan
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W238-W244; doi:10.1093/nar/gkm308 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shannan J. Ho Sui, Debra L. Fulton, David J. Arenillas, Andrew T. Kwon, and Wyeth W. Wasserman
oPOSSUM: integrated tools for analysis of regulatory motif over-representation
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: W245-W252; doi:10.1093/nar/gkm427 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Shaun Mahony and Panayiotis V. Benos
STAMP: a web tool for exploring DNA-binding motif similarities
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W253-W258; doi:10.1093/nar/gkm272 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jonathan M. Carlson, Arijit Chakravarty, Charles E. DeZiel, and Robert H. Gross
SCOPE: a web server for practical de novo motif discovery
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W259-W264; doi:10.1093/nar/gkm310 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Zhao Xu and Hao Wang
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W265-W268; doi:10.1093/nar/gkm286 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jean-François Lucier, Jonathan Perreault, Jean-François Noël, Gilles Boire, and Jean-Pierre Perreault
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures
Nucleic Acids Research Advance Access published on June 1, 2007
Nucl. Acids Res. 2007 35: W269-W274; doi:10.1093/nar/gkm313 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Guoqing Lu, Thaine Rowley, Rebecca Garten, and Ruben O. Donis
FluGenome: a web tool for genotyping influenza A virus
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W275-W279; doi:10.1093/nar/gkm365 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yiming Bao, Pavel Bolotov, Dmitry Dernovoy, Boris Kiryutin, and Tatiana Tatusova
FLAN: a web server for influenza virus genome annotation
Nucleic Acids Research Advance Access published on June 1, 2007
Nucl. Acids Res. 2007 35: W280-W284; doi:10.1093/nar/gkm354 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Rezarta Islamaj Dogan, Lise Getoor, W. John Wilbur, and Stephen M. Mount
SplicePort—An interactive splice-site analysis tool
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: W285-W291; doi:10.1093/nar/gkm407 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Zoé Lacroix, Christophe Legendre, Louiqa Raschid, and Ben Snyder
BIPASS: BioInformatics Pipeline Alternative Splicing Services
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W292-W296; doi:10.1093/nar/gkm344 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Sylvain Foissac and Michael Sammeth
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W297-W299; doi:10.1093/nar/gkm311 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Mugdha Khaladkar, Vivian Bellofatto, Jason T. L. Wang, Bin Tian, and Bruce A. Shapiro
RADAR: a web server for RNA data analysis and research
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W300-W304; doi:10.1093/nar/gkm253 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Eva Freyhult, Vincent Moulton, and Peter Clote
RNAbor: a web server for RNA structural neighbors
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W305-W309; doi:10.1093/nar/gkm255 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Anke Busch and Rolf Backofen
INFO-RNA—a server for fast inverse RNA folding satisfying sequence constraints
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: W310-W313; doi:10.1093/nar/gkm218 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, and Shengqi Wang
RSRE: RNA structural robustness evaluator
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: W314-W319; doi:10.1093/nar/gkm361 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Jens Reeder, Peter Steffen, and Robert Giegerich
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W320-W324; doi:10.1093/nar/gkm258 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Cagri Aksay, Raheleh Salari, Emre Karakoc, Can Alkan, and S. Cenk Sahinalp
taveRNA: a web suite for RNA algorithms and applications
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W325-W329; doi:10.1093/nar/gkm303 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alexander Kaiser, Jan Krüger, and Dirk J. Evers
RNA Movies 2: sequential animation of RNA secondary structures
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: W330-W334; doi:10.1093/nar/gkm309 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andreas R. Gruber, Richard Neuböck, Ivo L. Hofacker, and Stefan Washietl
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: W335-W338; doi:10.1093/nar/gkm222 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Peng Jiang, Haonan Wu, Wenkai Wang, Wei Ma, Xiao Sun, and Zuhong Lu
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: W339-W344; doi:10.1093/nar/gkm368 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shu-Qi Zhao, Liping Wei, and Ge Gao
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
Nucl. Acids Res. 2007 35: W345-W349; doi:10.1093/nar/gkm391 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Helena Tåquist, Yuanyuan Cui, and David H. Ardell
TFAM 1.0: an online tRNA function classifier
Nucleic Acids Research Advance Access published on June 25, 2007
Nucl. Acids Res. 2007 35: W350-W353; doi:10.1093/nar/gkm393 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jianlin Cheng
DOMAC: an accurate, hybrid protein domain prediction server
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: W354-W356; doi:10.1093/nar/gkm390 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Harianto Tjong, Sanbo Qin, and Huan-Xiang Zhou
PI2PE: protein interface/interior prediction engine
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W357-W362; doi:10.1093/nar/gkm231 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Narcis Fernandez-Fuentes, Carlos J. Madrid-Aliste, Brajesh Kumar Rai, J. Eduardo Fajardo, and András Fiser
M4T: a comparative protein structure modeling server
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W363-W368; doi:10.1093/nar/gkm341 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Björn Wallner, Per Larsson, and Arne Elofsson
Pcons.net: protein structure prediction meta server
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W369-W374; doi:10.1093/nar/gkm319 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ian W. Davis, Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura W. Murray, W. Bryan Arendall, III, Jack Snoeyink, Jane S. Richardson, and David C. Richardson
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: W375-W383; doi:10.1093/nar/gkm216 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alper Uzun, Chesley M. Leslin, Alexej Abyzov, and Valentin Ilyin
Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W384-W392; doi:10.1093/nar/gkm232 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marc A. Marti-Renom, Ursula Pieper, M. S. Madhusudhan, Andrea Rossi, Narayanan Eswar, Fred P. Davis, Fátima Al-Shahrour, Joaquín Dopazo, and Andrej Sali
DBAli tools: mining the protein structure space
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W393-W397; doi:10.1093/nar/gkm236 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kengo Kinoshita, Yoichi Murakami, and Haruki Nakamura
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: W398-W402; doi:10.1093/nar/gkm351 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Christian X. Weichenberger and Manfred J. Sippl
NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W403-W406; doi:10.1093/nar/gkm263 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Markus Wiederstein and Manfred J. Sippl
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W407-W410; doi:10.1093/nar/gkm290 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Stefan J. Suhrer, Markus Gruber, and Manfred J. Sippl
QSCOP-BLAST—fast retrieval of quantified structural information for protein sequences of unknown structure
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W411-W415; doi:10.1093/nar/gkm264 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, and Manuela Helmer-Citterich
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W416-W419; doi:10.1093/nar/gkm228 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yan-Long Lai, Shih-Chung Yen, Sung-Huan Yu, and Jenn-Kang Hwang
pKNOT: the protein KNOT web server
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W420-W424; doi:10.1093/nar/gkm304 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Grigory Kolesov, Peter Virnau, Mehran Kardar, and Leonid A. Mirny
Protein knot server: detection of knots in protein structures
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W425-W428; doi:10.1093/nar/gkm312 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Lukas Käll, Anders Krogh, and Erik L.L. Sonnhammer
Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: W429-W432; doi:10.1093/nar/gkm256 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, Jörg Hau, Olivier Martin, Dmitri Kuznetsov, and Laurent Falquet
MyHits: improvements to an interactive resource for analyzing protein sequences
Nucleic Acids Research Advance Access published on June 1, 2007
Nucl. Acids Res. 2007 35: W433-W437; doi:10.1093/nar/gkm352 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chi-Hua Tung and Jinn-Moon Yang
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W438-W443; doi:10.1093/nar/gkm288 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

C. del Val, P. Ernst, M Falkenhahn, C. Fladerer, K. H. Glatting, S. Suhai, and A. Hotz-Wagenblatt
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W444-W450; doi:10.1093/nar/gkm364 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, and Manuela Helmer-Citterich
SH3-Hunter: discovery of SH3 domain interaction sites in proteins
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W451-W454; doi:10.1093/nar/gkm296 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Norman E. Davey, Richard J. Edwards, and Denis C. Shields
The SLiMDisc server: short, linear motif discovery in proteins
Nucleic Acids Research Advance Access published on June 18, 2007
Nucl. Acids Res. 2007 35: W455-W459; doi:10.1093/nar/gkm400 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Takashi Ishida and Kengo Kinoshita
PrDOS: prediction of disordered protein regions from amino acid sequence
Nucleic Acids Research Advance Access published on June 12, 2007
Nucl. Acids Res. 2007 35: W460-W464; doi:10.1093/nar/gkm363 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chung-Tsai Su, Chien-Yu Chen, and Chen-Ming Hsu
iPDA: integrated protein disorder analyzer
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: W465-W472; doi:10.1093/nar/gkm353 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

K. G. Tina, R. Bhadra, and N. Srinivasan
PIC: Protein Interactions Calculator
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W473-W476; doi:10.1093/nar/gkm423 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Joel Franklin, Patrice Koehl, Sebastian Doniach, and Marc Delarue
MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape
Nucleic Acids Research Advance Access published on June 1, 2007
Nucl. Acids Res. 2007 35: W477-W482; doi:10.1093/nar/gkm342 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Ludovic Autin and Pierre Tufféry
PMG: online generation of high-quality molecular pictures and storyboarded animations
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W483-W488; doi:10.1093/nar/gkm277 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

C. Axel Innis
siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: W489-W494; doi:10.1093/nar/gkm422 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

K. Anton Feenstra, Walter Pirovano, Klaas Krab, and Jaap Heringa
Sequence harmony: detecting functional specificity from alignments
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W495-W498; doi:10.1093/nar/gkm406 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Harpreet Kaur Saini and Daniel Fischer
FRalanyzer: a tool for functional analysis of fold-recognition sequence–structure alignments
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W499-W502; doi:10.1093/nar/gkm367 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Kshama Goyal, Debasisa Mohanty, and Shekhar C. Mande
PAR-3D: a server to predict protein active site residues
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W503-W505; doi:10.1093/nar/gkm252 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Adi Stern, Adi Doron-Faigenboim, Elana Erez, Eric Martz, Eran Bacharach, and Tal Pupko
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: W506-W511; doi:10.1093/nar/gkm382 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Clifford E. Felder, Jaime Prilusky, Israel Silman, and Joel L. Sussman
A server and database for dipole moments of proteins
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W512-W521; doi:10.1093/nar/gkm307 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Todd J. Dolinsky, Paul Czodrowski, Hui Li, Jens E. Nielsen, Jan H. Jensen, Gerhard Klebe, and Nathan A. Baker
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W522-W525; doi:10.1093/nar/gkm276 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Shula Shazman, Gershon Celniker, Omer Haber, Fabian Glaser, and Yael Mandel-Gutfreund
Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W526-W530; doi:10.1093/nar/gkm401 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Mark V. Berjanskii and David S. Wishart
The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W531-W537; doi:10.1093/nar/gkm328 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jin-Rui Xu, Jing-Xian Zhang, Bu-Cong Han, Liang Liang, and Zhi-Liang Ji
CytoSVM: an advanced server for identification of cytokine-receptor interactions
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W538-W542; doi:10.1093/nar/gkm254 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Hani Neuvirth, Uri Heinemann, David Birnbaum, Naftali Tishby, and Gideon Schreiber
ProMateus—an open research approach to protein-binding sites analysis
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W543-W548; doi:10.1093/nar/gkm301 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Narendra Kumar and Debasisa Mohanty
MODPROPEP: a program for knowledge-based modeling of protein–peptide complexes
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W549-W555; doi:10.1093/nar/gkm266 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

P. Christoph Champ and Carlos J. Camacho
FastContact: a free energy scoring tool for protein–protein complex structures
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W556-W560; doi:10.1093/nar/gkm326 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yung-Chiang Chen, Yu-Shu Lo, Wen-Chang Hsu, and Jinn-Moon Yang
3D-partner: a web server to infer interacting partners and binding models
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W561-W567; doi:10.1093/nar/gkm346 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

T. Bohme Leite, D. Gomes, M.A. Miteva, J. Chomilier, B.O. Villoutreix, and P. Tufféry
Frog: a FRee Online druG 3D conformation generator
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W568-W572; doi:10.1093/nar/gkm289 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Gonzalo López, Alfonso Valencia, and Michael L. Tress
firestar—prediction of functionally important residues using structural templates and alignment reliability
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W573-W577; doi:10.1093/nar/gkm297 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant Honavar, and Drena Dobbs
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: W578-W584; doi:10.1093/nar/gkm294 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai
WoLF PSORT: protein localization predictor
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W585-W587; doi:10.1093/nar/gkm259 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yung-Hao Wong, Tzong-Yi Lee, Han-Kuen Liang, Chia-Mao Huang, Ting-Yuan Wang, Yi-Huan Yang, Chia-Huei Chu, Hsien-Da Huang, Ming-Tat Ko, and Jenn-Kang Hwang
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W588-W594; doi:10.1093/nar/gkm322 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Joshua S. Kaminker, Yan Zhang, Colin Watanabe, and Zemin Zhang
CanPredict: a computational tool for predicting cancer-associated missense mutations
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W595-W598; doi:10.1093/nar/gkm405 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, and Drena Dobbs
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W599-W605; doi:10.1093/nar/gkm349 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Eoin Fahy, Manish Sud, Dawn Cotter, and Shankar Subramaniam
LIPID MAPS online tools for lipid research
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W606-W612; doi:10.1093/nar/gkm324 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Thomas Handorf and Oliver Ebenhöh
MetaPath Online: a web server implementation of the network expansion algorithm
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: W613-W618; doi:10.1093/nar/gkm287 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jost Degenhardt, Martin Haubrock, Jürgen Dönitz, Edgar Wingender, and Torsten Crass
DEEP—A tool for differential expression effector prediction
Nucleic Acids Research Advance Access published on June 21, 2007
Nucl. Acids Res. 2007 35: W619-W624; doi:10.1093/nar/gkm469 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart, and Charles DeLisi
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: W625-W632; doi:10.1093/nar/gkm295 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Feng-Chi Chen, Chueng-Jong Chen, and Trees-Juen Chuang
INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W633-W638; doi:10.1093/nar/gkm350 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yun-Sheng Chung, Wei-Hsun Lee, Chuan Yi Tang, and Chin Lung Lu
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W639-W644; doi:10.1093/nar/gkm275 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sebastien Moretti, Fabrice Armougom, Iain M. Wallace, Desmond G. Higgins, Cornelius V. Jongeneel, and Cedric Notredame
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods
Nucleic Acids Research Advance Access published on May 25, 2007
Nucl. Acids Res. 2007 35: W645-W648; doi:10.1093/nar/gkm333 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Jimin Pei, Bong-Hyun Kim, Ming Tang, and Nick V. Grishin
PROMALS web server for accurate multiple protein sequence alignments
Nucleic Acids Research Advance Access published on April 22, 2007
Nucl. Acids Res. 2007 35: W649-W652; doi:10.1093/nar/gkm227 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Ruslan I. Sadreyev, Ming Tang, Bong-Hyun Kim, and Nick V. Grishin
COMPASS server for remote homology inference
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W653-W658; doi:10.1093/nar/gkm293 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

F. Ferrè, Y. Ponty, W. A. Lorenz, and Peter Clote
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities
Nucleic Acids Research Advance Access published on June 13, 2007
Nucl. Acids Res. 2007 35: W659-W668; doi:10.1093/nar/gkm334 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, and Inna Dubchak
Multiple whole genome alignments and novel biomedical applications at the VISTA portal
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W669-W674; doi:10.1093/nar/gkm279 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Satish Chikkagoudar, Usman Roshan, and Dennis Livesay
eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities
Nucleic Acids Research Advance Access published on May 7, 2007
Nucl. Acids Res. 2007 35: W675-W677; doi:10.1093/nar/gkm267 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Yi Zhou and Laura F. Landweber
BLASTO: a tool for searching orthologous groups
Nucleic Acids Research Advance Access published on May 5, 2007
Nucl. Acids Res. 2007 35: W678-W682; doi:10.1093/nar/gkm278 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Andreas Keller, Nicole Comtesse, Nicole Ludwig, Eckart Meese, and Hans-Peter Lenhof
SePaCS—a web-based application for classification of seroreactivity profiles
Nucleic Acids Research Advance Access published on May 3, 2007
Nucl. Acids Res. 2007 35: W683-W687; doi:10.1093/nar/gkm262 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material]  

Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, and Rolf Backofen
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W688-W693; doi:10.1093/nar/gkm292 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Alvaro Martinez Barrio, Daniel Soeria-Atmadja, Anders Nistér, Mats G. Gustafsson, Ulf Hammerling, and Erik Bongcam-Rudloff
EVALLER: a web server for in silico assessment of potential protein allergenicity
Nucleic Acids Research Advance Access published on May 30, 2007
Nucl. Acids Res. 2007 35: W694-W700; doi:10.1093/nar/gkm370 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Leonid Zamdborg, Richard D. LeDuc, Kevin J. Glowacz, Yong-Bin Kim, Vinayak Viswanathan, Ian T. Spaulding, Bryan P. Early, Eric J. Bluhm, Shannee Babai, and Neil L. Kelleher
ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry
Nucleic Acids Research Advance Access published on June 22, 2007
Nucl. Acids Res. 2007 35: W701-W706; doi:10.1093/nar/gkm371 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Chuan-Yih Yu, Yin-Hao Tsui, Yi-Hwa Yian, Ting-Yi Sung, and Wen-Lian Hsu
The Multi-Q web server for multiplexed protein quantitation
Nucleic Acids Research Advance Access published on June 6, 2007
Nucl. Acids Res. 2007 35: W707-W712; doi:10.1093/nar/gkm345 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Sik Lok Lam
DSHIFT: a web server for predicting DNA chemical shifts
Nucleic Acids Research Advance Access published on May 21, 2007
Nucl. Acids Res. 2007 35: W713-W717; doi:10.1093/nar/gkm320 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Trias Thireou, Vassilis Atlamazoglou, Manolis Levakis, Elias Eliopoulos, Athanassios Hountas, George Tsoucaris, and Kostas Bethanis
CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography
Nucleic Acids Research Advance Access published on May 8, 2007
Nucl. Acids Res. 2007 35: W718-W722; doi:10.1093/nar/gkm225 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

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