Nucleic Acids Research

Editorial

Gary Benson

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

Articles

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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] [Supplementary Material]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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]  

Get checked abstract 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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