Articles:

Joanne A. Fox, Scott McMillan, and B. F. Francis Ouellette

A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory
Nucl. Acids Res. 2006 34: W3-W5; doi:10.1093/nar/gkl379 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Web Server Summaries] [Request Permissions]  

Jian Ye, Scott McGinnis, and Thomas L. Madden

BLAST: improvements for better sequence analysis
Nucl. Acids Res. 2006 34: W6-W9; doi:10.1093/nar/gkl164 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jeanette Tĺngrot, Lixiao Wang, Bo Kĺgström, and Uwe H. Sauer

FISH—family identification of sequence homologues using structure anchored hidden Markov models
Nucl. Acids Res. 2006 34: W10-W14; doi:10.1093/nar/gkl330 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Markus Rampp, Thomas Soddemann, and Hermann Lederer

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis
Nucl. Acids Res. 2006 34: W15-W19; doi:10.1093/nar/gkl254 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, and Haruki Nakamura

PreBI: prediction of biological interfaces of proteins in crystals
Nucl. Acids Res. 2006 34: W20-W24; doi:10.1093/nar/gkl267 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hanjo Täubig, Arno Buchner, and Jan Griebsch

PAST: fast structure-based searching in the PDB
Nucl. Acids Res. 2006 34: W20-W23; doi:10.1093/nar/gkl273 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lee-Wei Yang, A. J. Rader, Xiong Liu, Cristopher Jon Jursa, Shann Ching Chen, Hassan A. Karimi, and Ivet Bahar

oGNM: online computation of structural dynamics using the Gaussian Network Model
Nucl. Acids Res. 2006 34: W24-W31; doi:10.1093/nar/gkl084 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Z. R. Li, H. H. Lin, L. Y. Han, L. Jiang, X. Chen, and Y. Z. Chen

PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
Nucl. Acids Res. 2006 34: W32-W37; doi:10.1093/nar/gkl305 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Cyril Azuara, Erik Lindahl, Patrice Koehl, Henri Orland, and Marc Delarue

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson–Boltzmann treatment of macromolecule electrostatics
Nucl. Acids Res. 2006 34: W38-W42; doi:10.1093/nar/gkl072 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexander A. Kantardjiev and Boris P. Atanasov

PHEPS: web-based pH-dependent Protein Electrostatics Server
Nucl. Acids Res. 2006 34: W43-W47; doi:10.1093/nar/gkl165 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Barbara M. Tynan-Connolly and Jens Erik Nielsen

pKD: re-designing protein pK_a values
Nucl. Acids Res. 2006 34: W48-W51; doi:10.1093/nar/gkl192 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erik Lindahl, Cyril Azuara, Patrice Koehl, and Marc Delarue

NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
Nucl. Acids Res. 2006 34: W52-W56; doi:10.1093/nar/gkl082 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yunho Jang, Jay I. Jeong, and Moon K. Kim

UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models
Nucl. Acids Res. 2006 34: W57-W62; doi:10.1093/nar/gkl039 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mark V. Berjanskii, Stephen Neal, and David S. Wishart

PREDITOR: a web server for predicting protein torsion angle restraints
Nucl. Acids Res. 2006 34: W63-W69; doi:10.1093/nar/gkl341 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Michael Gromiha, A. Mary Thangakani, and S. Selvaraj

FOLD-RATE: prediction of protein folding rates from amino acid sequence
Nucl. Acids Res. 2006 34: W70-W74; doi:10.1093/nar/gkl043 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J.-C. Gelly, C. Etchebest, S. Hazout, and A.G. de Brevern

Protein Peeling 2: a web server to convert protein structures into series of protein units
Nucl. Acids Res. 2006 34: W75-W78; doi:10.1093/nar/gkl292 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

R. R. Gabdoulline, S. Ulbrich, S. Richter, and R. C. Wade

ProSAT2—Protein Structure Annotation Server
Nucl. Acids Res. 2006 34: W79-W83; doi:10.1093/nar/gkl216 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rasmus Wernersson, Kristoffer Rapacki, Hans-Henrik Stćrfeldt, Peter Wad Sackett, and Anne Mřlgaard

FeatureMap3D—a tool to map protein features and sequence conservation onto homologous structures in the PDB
Nucl. Acids Res. 2006 34: W84-W88; doi:10.1093/nar/gkl227 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jui-Hung Hung, Hsien-Da Huang, and Tzong-Yi Lee

ProKware: integrated software for presenting protein structural properties in protein tertiary structures
Nucl. Acids Res. 2006 34: W89-W94; doi:10.1093/nar/gkl235 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Edward S. C. Shih, Ruei-chi R. Gan, and Ming-Jing Hwang

OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures
Nucl. Acids Res. 2006 34: W95-W98; doi:10.1093/nar/gkl264 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sunghoon Lee, Byungwook Lee, Insoo Jang, Sangsoo Kim, and Jong Bhak

Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information
Nucl. Acids Res. 2006 34: W99-W103; doi:10.1093/nar/gkl351 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Blaise T. F. Alako, Daphne Rainey, Harm Nijveen, and Jack A. M. Leunissen

TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure
Nucl. Acids Res. 2006 34: W104-W109; doi:10.1093/nar/gkl171 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Angel Carro, Michael Tress, David de Juan, Florencio Pazos, Pedro Lopez-Romero, Antonio del Sol, Alfonso Valencia, and Ana M. Rojas

TreeDet: a web server to explore sequence space
Nucl. Acids Res. 2006 34: W110-W115; doi:10.1093/nar/gkl203 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Joe Dundas, Zheng Ouyang, Jeffery Tseng, Andrew Binkowski, Yaron Turpaz, and Jie Liang

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
Nucl. Acids Res. 2006 34: W116-W118; doi:10.1093/nar/gkl282 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Tyagi, P. Sharma, C. S. Swamy, F. Cadet, N. Srinivasan, A. G. de Brevern, and B. Offmann

Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet
Nucl. Acids Res. 2006 34: W119-W123; doi:10.1093/nar/gkl199 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shandar Ahmad, Hidetoshi Kono, Marcos J. Araúzo-Bravo, and Akinori Sarai

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein–DNA recognition
Nucl. Acids Res. 2006 34: W124-W127; doi:10.1093/nar/gkl104 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

K. Sumathi, P. Ananthalakshmi, M. N. A. Md. Roshan, and K. Sekar

3dSS: 3D structural superposition
Nucl. Acids Res. 2006 34: W128-W132; doi:10.1093/nar/gkl036 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hatice Gulcin Ozer and William C. Ray

MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments
Nucl. Acids Res. 2006 34: W133-W136; doi:10.1093/nar/gkl251 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Johannes Söding, Michael Remmert, and Andreas Biegert

HHrep: de novo protein repeat detection and the origin of TIM barrels
Nucl. Acids Res. 2006 34: W137-W142; doi:10.1093/nar/gkl130 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

R. Bhadra, S. Sandhya, K. R. Abhinandan, S. Chakrabarti, R. Sowdhamini, and N. Srinivasan

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains
Nucl. Acids Res. 2006 34: W143-W146; doi:10.1093/nar/gkl157 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Julien Maupetit, R. Gautier, and Pierre Tufféry

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace
Nucl. Acids Res. 2006 34: W147-W151; doi:10.1093/nar/gkl289 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chih-Chieh Chen, Jenn-Kang Hwang, and Jinn-Moon Yang

(PS)²: protein structure prediction server
Nucl. Acids Res. 2006 34: W152-W157; doi:10.1093/nar/gkl187 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Lusheng Chen, Wei Wang, Shaoping Ling, Caiyan Jia, and Fei Wang

KemaDom: a web server for domain prediction using kernel machine with local context
Nucl. Acids Res. 2006 34: W158-W163; doi:10.1093/nar/gkl331 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alessandro Vullo, Oscar Bortolami, Gianluca Pollastri, and Silvio C. E. Tosatto

Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines
Nucl. Acids Res. 2006 34: W164-W168; doi:10.1093/nar/gkl166 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mauro Amico, Michele Finelli, Ivan Rossi, Andrea Zauli, Arne Elofsson, Hĺkan Viklund, Gunnar von Heijne, David Jones, Anders Krogh, Piero Fariselli, Pier Luigi Martelli, and Rita Casadio

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins
Nucl. Acids Res. 2006 34: W169-W172; doi:10.1093/nar/gkl208 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Narcis Fernandez-Fuentes, Jun Zhai, and András Fiser

ArchPRED: a template based loop structure prediction server
Nucl. Acids Res. 2006 34: W173-W176; doi:10.1093/nar/gkl113 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alessio Ceroni, Andrea Passerini, Alessandro Vullo, and Paolo Frasconi

DISULFIND: a disulfide bonding state and cysteine connectivity prediction server
Nucl. Acids Res. 2006 34: W177-W181; doi:10.1093/nar/gkl266 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

F. Ferrč and P. Clote

DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification
Nucl. Acids Res. 2006 34: W182-W185; doi:10.1093/nar/gkl189 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Henry Bigelow and Burkhard Rost

PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins
Nucl. Acids Res. 2006 34: W186-W188; doi:10.1093/nar/gkl262 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

J. Waldispühl, Bonnie Berger, Peter Clote, and Jean-Marc Steyaert

transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels
Nucl. Acids Res. 2006 34: W189-W193; doi:10.1093/nar/gkl205 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Pierre Dönnes and Oliver Kohlbacher

SVMHC: a server for prediction of MHC-binding peptides
Nucl. Acids Res. 2006 34: W194-W197; doi:10.1093/nar/gkl284 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tun-Wen Pai, Margaret Dah-Tsyr Chang, Wen-Shyong Tzou, Bo-Han Su, Pei-Chih Wu, Hao-Teng Chang, and Wei-I Chou

R_EMUS: a tool for identification of unique peptide segments as epitopes
Nucl. Acids Res. 2006 34: W198-W201; doi:10.1093/nar/gkl188 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sudipto Saha and G. P. S. Raghava

AlgPred: prediction of allergenic proteins and mapping of IgE epitopes
Nucl. Acids Res. 2006 34: W202-W209; doi:10.1093/nar/gkl343 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chittibabu Guda

pTARGET: a web server for predicting protein subcellular localization
Nucl. Acids Res. 2006 34: W210-W213; doi:10.1093/nar/gkl093 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maria Novatchkova, Georg Schneider, Richard Fritz, Frank Eisenhaber, and Alexander Schleiffer

DOUTfinder—identification of distant domain outliers using subsignificant sequence similarity
Nucl. Acids Res. 2006 34: W214-W218; doi:10.1093/nar/gkl332 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Honglin Li, Zhenting Gao, Ling Kang, Hailei Zhang, Kun Yang, Kunqian Yu, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Jianhua Shen, Xicheng Wang, and Hualiang Jiang

TarFisDock: a web server for identifying drug targets with docking approach
Nucl. Acids Res. 2006 34: W219-W224; doi:10.1093/nar/gkl114 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ana P. C. Rodrigues, Barry J. Grant, and Roderick E. Hubbard

sgTarget: a target selection resource for structural genomics
Nucl. Acids Res. 2006 34: W225-W230; doi:10.1093/nar/gkl121 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

G. Pugalenthi, K. Shameer, N. Srinivasan, and R. Sowdhamini

HARMONY: a server for the assessment of protein structures
Nucl. Acids Res. 2006 34: W231-W234; doi:10.1093/nar/gkl314 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yi Liu and Brian Kuhlman

RosettaDesign server for protein design
Nucl. Acids Res. 2006 34: W235-W238; doi:10.1093/nar/gkl163 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Vijaya Parthiban, M. Michael Gromiha, and Dietmar Schomburg

CUPSAT: prediction of protein stability upon point mutations
Nucl. Acids Res. 2006 34: W239-W242; doi:10.1093/nar/gkl190 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Liangjiang Wang and Susan J. Brown

BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences
Nucl. Acids Res. 2006 34: W243-W248; doi:10.1093/nar/gkl298 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hu Chen, Yu Xue, Ni Huang, Xuebiao Yao, and Zhirong Sun

MeMo: a web tool for prediction of protein methylation modifications
Nucl. Acids Res. 2006 34: W249-W253; doi:10.1093/nar/gkl233 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yu Xue, Fengfeng Zhou, Chuanhai Fu, Ying Xu, and Xuebiao Yao

SUMOsp: a web server for sumoylation site prediction
Nucl. Acids Res. 2006 34: W254-W257; doi:10.1093/nar/gkl207 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Sangtae Kim, Seungjin Na, Ji Woong Sim, Heejin Park, Jaeho Jeong, Hokeun Kim, Younghwan Seo, Jawon Seo, Kong-Joo Lee, and Eunok Paek

MODⁱ : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra
Nucl. Acids Res. 2006 34: W258-W263; doi:10.1093/nar/gkl245 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Nagarajan Harish, Rekha Gupta, Parul Agarwal, Vinod Scaria, and Beena Pillai

DyNAVacS: an integrative tool for optimized DNA vaccine design
Nucl. Acids Res. 2006 34: W264-W266; doi:10.1093/nar/gkl242 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Bruce R. Southey, Andinet Amare, Tyler A. Zimmerman, Sandra L. Rodriguez-Zas, and Jonathan V. Sweedler

NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides
Nucl. Acids Res. 2006 34: W267-W272; doi:10.1093/nar/gkl161 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Anne de Jong, Sacha A. F. T. van Hijum, Jetta J. E. Bijlsma, Jan Kok, and Oscar P. Kuipers

BAGEL: a web-based bacteriocin genome mining tool
Nucl. Acids Res. 2006 34: W273-W279; doi:10.1093/nar/gkl237 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shu Ju Hsieh, Chun Yuan Lin, Ning Han Liu, Wei Yuan Chow, and Chuan Yi Tang

GeneAlign: a coding exon prediction tool based on phylogenetical comparisons
Nucl. Acids Res. 2006 34: W280-W284; doi:10.1093/nar/gkl307 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Simona Rossi, Daniele Masotti, Christine Nardini, Elena Bonora, Giovanni Romeo, Enrico Macii, Luca Benini, and Stefano Volinia

TOM: a web-based integrated approach for identification of candidate disease genes
Nucl. Acids Res. 2006 34: W285-W292; doi:10.1093/nar/gkl340 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jia Ye, Lin Fang, Hongkun Zheng, Yong Zhang, Jie Chen, Zengjin Zhang, Jing Wang, Shengting Li, Ruiqiang Li, Lars Bolund, and Jun Wang

WEGO: a web tool for plotting GO annotations
Nucl. Acids Res. 2006 34: W293-W297; doi:10.1093/nar/gkl031 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Carlos Prieto and Javier De Las Rivas

APID: Agile Protein Interaction DataAnalyzer
Nucl. Acids Res. 2006 34: W298-W302; doi:10.1093/nar/gkl128 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Darby Tien-Hao Chang, Yi-Zhong Weng, Jung-Hsin Lin, Ming-Jing Hwang, and Yen-Jen Oyang

Protemot: prediction of protein binding sites with automatically extracted geometrical templates
Nucl. Acids Res. 2006 34: W303-W309; doi:10.1093/nar/gkl344 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andrey Tovchigrechko and Ilya A. Vakser

GRAMM-X public web server for protein–protein docking
Nucl. Acids Res. 2006 34: W310-W314; doi:10.1093/nar/gkl206 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

José M. G. Izarzugaza, David Juan, Carles Pons, Juan A. G. Ranea, Alfonso Valencia, and Florencio Pazos

TSEMA: interactive prediction of protein pairings between interacting families
Nucl. Acids Res. 2006 34: W315-W319; doi:10.1093/nar/gkl112 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Laetitia Martin, Vincent Catherinot, and Gilles Labesse

kinDOCK: a tool for comparative docking of protein kinase ligands
Nucl. Acids Res. 2006 34: W325-W329; doi:10.1093/nar/gkl211 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christopher J. Penkett, James A. Morris, Valerie Wood, and Jürg Bähler

YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms
Nucl. Acids Res. 2006 34: W330-W334; doi:10.1093/nar/gkl311 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Andreas Biegert, Christian Mayer, Michael Remmert, Johannes Söding, and Andrei N. Lupas

The MPI Bioinformatics Toolkit for protein sequence analysis
Nucl. Acids Res. 2006 34: W335-W339; doi:10.1093/nar/gkl217 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Naveed Massjouni, Corban G. Rivera, and T. M. Murali

VIRGO: computational prediction of gene functions
Nucl. Acids Res. 2006 34: W340-W344; doi:10.1093/nar/gkl225 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chisato Yamasaki, Hiroaki Kawashima, Fusano Todokoro, Yasuhiro Imamizu, Makoto Ogawa, Motohiko Tanino, Takeshi Itoh, Takashi Gojobori, and Tadashi Imanishi

TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
Nucl. Acids Res. 2006 34: W345-W349; doi:10.1093/nar/gkl283 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Victor Neduva and Robert B. Russell

DILIMOT: discovery of linear motifs in proteins
Nucl. Acids Res. 2006 34: W350-W355; doi:10.1093/nar/gkl159 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Chen-Ming Hsu, Chien-Yu Chen, and Baw-Jhiune Liu

MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences
Nucl. Acids Res. 2006 34: W356-W361; doi:10.1093/nar/gkl309 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Edouard de Castro, Christian J. A. Sigrist, Alexandre Gattiker, Virginie Bulliard, Petra S. Langendijk-Genevaux, Elisabeth Gasteiger, Amos Bairoch, and Nicolas Hulo

ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins
Nucl. Acids Res. 2006 34: W362-W365; doi:10.1093/nar/gkl124 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Shane Neph and Martin Tompa

MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes
Nucl. Acids Res. 2006 34: W366-W368; doi:10.1093/nar/gkl069 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Timothy L. Bailey, Nadya Williams, Chris Misleh, and Wilfred W. Li

MEME: discovering and analyzing DNA and protein sequence motifs
Nucl. Acids Res. 2006 34: W369-W373; doi:10.1093/nar/gkl198 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Johannes Söding, Michael Remmert, Andreas Biegert, and Andrei N. Lupas

HHsenser: exhaustive transitive profile search using HMM–HMM comparison
Nucl. Acids Res. 2006 34: W374-W378; doi:10.1093/nar/gkl195 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Iddo Friedberg, Tim Harder, and Adam Godzik

JAFA: a protein function annotation meta-server
Nucl. Acids Res. 2006 34: W379-W381; doi:10.1093/nar/gkl045 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Han Liang, Weihua Zhou, and Laura F. Landweber

SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
Nucl. Acids Res. 2006 34: W382-W384; doi:10.1093/nar/gkl272 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Rasmus Wernersson

Virtual Ribosome—a comprehensive DNA translation tool with support for integration of sequence feature annotation
Nucl. Acids Res. 2006 34: W385-W388; doi:10.1093/nar/gkl252 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Federico Abascal, Rafael Zardoya, and David Posada

GenDecoder: genetic code prediction for metazoan mitochondria
Nucl. Acids Res. 2006 34: W389-W393; doi:10.1093/nar/gkl044 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

T. Z. DeSantis, Jr, P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, and G. L. Andersen

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
Nucl. Acids Res. 2006 34: W394-W399; doi:10.1093/nar/gkl244 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tobias Dezulian, Martin Schaefer, Roland Wiese, Detlef Weigel, and Daniel H. Huson

CrossLink: visualization and exploration of sequence relationships between (micro) RNAs
Nucl. Acids Res. 2006 34: W400-W404; doi:10.1093/nar/gkl223 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Eckart Bindewald, Thomas D. Schneider, and Bruce A. Shapiro

CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
Nucl. Acids Res. 2006 34: W405-W411; doi:10.1093/nar/gkl269 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Oranit Dror, Ruth Nussinov, and Haim J. Wolfson

The ARTS web server for aligning RNA tertiary structures
Nucl. Acids Res. 2006 34: W412-W415; doi:10.1093/nar/gkl312 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yanga Byun and Kyungsook Han

PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures
Nucl. Acids Res. 2006 34: W416-W422; doi:10.1093/nar/gkl210 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tzu-Hao Chang, Hsien-Da Huang, Tzu-Neng Chuang, Dray-Ming Shien, and Jorng-Tzong Horng

RNAMST: efficient and flexible approach for identifying RNA structural homologs
Nucl. Acids Res. 2006 34: W423-W428; doi:10.1093/nar/gkl231 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hsi-Yuan Huang, Chia-Hung Chien, Kuan-Hua Jen, and Hsien-Da Huang

RegRNA: an integrated web server for identifying regulatory RNA motifs and elements
Nucl. Acids Res. 2006 34: W429-W434; doi:10.1093/nar/gkl333 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mario Stanke, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, and Burkhard Morgenstern

AUGUSTUS: ab initio prediction of alternative transcripts
Nucl. Acids Res. 2006 34: W435-W439; doi:10.1093/nar/gkl200 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Tiziana Castrignanň, Raffaella Rizzi, Ivano Giuseppe Talamo, Paolo D'Onorio De Meo, Anna Anselmo, Paola Bonizzoni, and Graziano Pesole

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization
Nucl. Acids Res. 2006 34: W440-W443; doi:10.1093/nar/gkl324 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Durgaprasad Bollina, Bernett T. K. Lee, Tin Wee Tan, and Shoba Ranganathan

ASGS: an alternative splicing graph web service
Nucl. Acids Res. 2006 34: W444-W447; doi:10.1093/nar/gkl268 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yuki Naito, Kumiko Ui-Tei, Toru Nishikawa, Yutaka Takebe, and Kaoru Saigo

siVirus: web-based antiviral siRNA design software for highly divergent viral sequences
Nucl. Acids Res. 2006 34: W448-W450; doi:10.1093/nar/gkl214 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Jan Krüger and Marc Rehmsmeier

RNAhybrid: microRNA target prediction easy, fast and flexible
Nucl. Acids Res. 2006 34: W451-W454; doi:10.1093/nar/gkl243 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jin-Wu Nam, Jinhan Kim, Sung-Kyu Kim, and Byoung-Tak Zhang

ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
Nucl. Acids Res. 2006 34: W455-W458; doi:10.1093/nar/gkl321 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ali Masoudi-Nejad, Koichiro Tonomura, Shuichi Kawashima, Yuki Moriya, Masanori Suzuki, Masumi Itoh, Minoru Kanehisa, Takashi Endo, and Susumu Goto

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments
Nucl. Acids Res. 2006 34: W459-W462; doi:10.1093/nar/gkl066 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ming Zhang, Anne-Kathrin Schultz, Charles Calef, Carla Kuiken, Thomas Leitner, Bette Korber, Burkhard Morgenstern, and Mario Stanke

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
Nucl. Acids Res. 2006 34: W463-W465; doi:10.1093/nar/gkl255 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Michael Baitaluk, Mayya Sedova, Animesh Ray, and Amarnath Gupta

BiologicalNetworks: visualization and analysis tool for systems biology
Nucl. Acids Res. 2006 34: W466-W471; doi:10.1093/nar/gkl308 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fátima Al-Shahrour, Pablo Minguez, Joaquín Tárraga, David Montaner, Eva Alloza, Juan M. Vaquerizas, Lucía Conde, Christian Blaschke, Javier Vera, and Joaquín Dopazo

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments
Nucl. Acids Res. 2006 34: W472-W476; doi:10.1093/nar/gkl172 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Stéphane Liva, Philippe Hupé, Pierre Neuvial, Isabel Brito, Eric Viara, Philippe La Rosa, and Emmanuel Barillot

CAPweb: a bioinformatics CGH array Analysis Platform
Nucl. Acids Res. 2006 34: W477-W481; doi:10.1093/nar/gkl215 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

F. Ferrč and P. Clote

BTW: a web server for Boltzmann time warping of gene expression time series
Nucl. Acids Res. 2006 34: W482-W485; doi:10.1093/nar/gkl162 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

David Montaner, Joaquín Tárraga, Jaime Huerta-Cepas, Jordi Burguet, Juan M. Vaquerizas, Lucía Conde, Pablo Minguez, Javier Vera, Sach Mukherjee, Joan Valls, Miguel A. G. Pujana, Eva Alloza, Javier Herrero, Fátima Al-Shahrour, and Joaquín Dopazo

Next station in microarray data analysis: GEPAS
Nucl. Acids Res. 2006 34: W486-W491; doi:10.1093/nar/gkl197 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Yu-Peng Wang, Liang Liang, Bu-Cong Han, Yu Quan, Xiao Wang, Tao Tao, and Zhi-Liang Ji

GEPS: the Gene Expression Pattern Scanner
Nucl. Acids Res. 2006 34: W492-W497; doi:10.1093/nar/gkl067 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Johannes Rainer, Fatima Sanchez-Cabo, Gernot Stocker, Alexander Sturn, and Zlatko Trajanoski

CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis
Nucl. Acids Res. 2006 34: W498-W503; doi:10.1093/nar/gkl038 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Iain W. Manfield, Chih-Hung Jen, John W. Pinney, Ioannis Michalopoulos, James R. Bradford, Philip M. Gilmartin, and David R. Westhead

Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis
Nucl. Acids Res. 2006 34: W504-W509; doi:10.1093/nar/gkl204 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maurice Scheer, Frank Klawonn, Richard Münch, Andreas Grote, Karsten Hiller, Claudia Choi, Ina Koch, Max Schobert, Elisabeth Härtig, Ulrich Klages, and Dieter Jahn

JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information
Nucl. Acids Res. 2006 34: W510-W515; doi:10.1093/nar/gkl329 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jeffrey G. Mandell and Carlos F. Barbas, III

Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases
Nucl. Acids Res. 2006 34: W516-W523; doi:10.1093/nar/gkl209 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Ian J. Donaldson and Berthold Göttgens

TFBScluster web server for the identification of mammalian composite regulatory elements
Nucl. Acids Res. 2006 34: W524-W528; doi:10.1093/nar/gkl041 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jan Grau, Irad Ben-Gal, Stefan Posch, and Ivo Grosse

VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees
Nucl. Acids Res. 2006 34: W529-W533; doi:10.1093/nar/gkl212 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Matti Kankainen, Petri Pehkonen, Päivi Rosenstöm, Petri Törönen, Garry Wong, and Liisa Holm

POXO: a web-enabled tool series to discover transcription factor binding sites
Nucl. Acids Res. 2006 34: W534-W540; doi:10.1093/nar/gkl296 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

T. Waleev, D. Shtokalo, T. Konovalova, N. Voss, E. Cheremushkin, P. Stegmaier, O. Kel-Margoulis, E. Wingender, and A. Kel

Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm
Nucl. Acids Res. 2006 34: W541-W545; doi:10.1093/nar/gkl342 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Thomas Fiedler and Marc Rehmsmeier

jPREdictor: a versatile tool for the prediction of cis-regulatory elements
Nucl. Acids Res. 2006 34: W546-W550; doi:10.1093/nar/gkl250 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Xuwo Ji, Wei Li, Jun Song, Liping Wei, and X. Shirley Liu

CEAS: cis-regulatory element annotation system
Nucl. Acids Res. 2006 34: W551-W554; doi:10.1093/nar/gkl322 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Saurabh Sinha, Yupu Liang, and Eric Siggia

Stubb: a program for discovery and analysis of cis-regulatory modules
Nucl. Acids Res. 2006 34: W555-W559; doi:10.1093/nar/gkl224 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Peter Luykx, Ivan V. Bajic, and Sawsan Khuri

NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors
Nucl. Acids Res. 2006 34: W560-W565; doi:10.1093/nar/gkl158 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Giulio Pavesi, Paolo Mereghetti, Federico Zambelli, Marco Stefani, Giancarlo Mauri, and Graziano Pesole

MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
Nucl. Acids Res. 2006 34: W566-W570; doi:10.1093/nar/gkl285 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Chun-Chi Liu, Chin-Chung Lin, Wen-Shyen E. Chen, Hsuan-Yu Chen, Pei-Chun Chang, Jeremy J.W. Chen, and Pan-Chyr Yang

CRSD: a comprehensive web server for composite regulatory signature discovery
Nucl. Acids Res. 2006 34: W571-W577; doi:10.1093/nar/gkl279 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Aurélie Lardenois, Frédéric Chalmel, Laurent Bianchetti, José-Alain Sahel, Thierry Léveillard, and Olivier Poch

PromAn: an integrated knowledge-based web server dedicated to promoter analysis
Nucl. Acids Res. 2006 34: W578-W583; doi:10.1093/nar/gkl193 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sarita Ranjan, Jayshree Seshadri, Vaibhav Vindal, Sailu Yellaboina, and Akash Ranjan

iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species
Nucl. Acids Res. 2006 34: W584-W587; doi:10.1093/nar/gkl202 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

M. Tech, B. Morgenstern, and P. Meinicke

TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites
Nucl. Acids Res. 2006 34: W588-W590; doi:10.1093/nar/gkl313 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Igor V. Deyneko, Björn Bredohl, Daniel Wesely, Yulia M. Kalybaeva, Alexander E. Kel, Helmut Blöcker, and Gerhard Kauer

FeatureScan: revealing property-dependent similarity of nucleotide sequences
Nucl. Acids Res. 2006 34: W591-W595; doi:10.1093/nar/gkl337 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Timo Lassmann and Erik L. L. Sonnhammer

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment
Nucl. Acids Res. 2006 34: W596-W599; doi:10.1093/nar/gkl191 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sébastien Moretti, Frédéric Reinier, Olivier Poirot, Fabrice Armougom, Stéphane Audic, Vladimir Keduas, and Cédric Notredame

PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments
Nucl. Acids Res. 2006 34: W600-W603; doi:10.1093/nar/gkl170 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fabrice Armougom, Sébastien Moretti, Olivier Poirot, Stéphane Audic, Pierre Dumas, Basile Schaeli, Vladimir Keduas, and Cedric Notredame

Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
Nucl. Acids Res. 2006 34: W604-W608; doi:10.1093/nar/gkl092 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Mikita Suyama, David Torrents, and Peer Bork

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Nucl. Acids Res. 2006 34: W609-W612; doi:10.1093/nar/gkl315 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Neil C. Jones, Degui Zhi, and Benjamin J. Raphael

AliWABA: alignment on the web through an A-Bruijn approach
Nucl. Acids Res. 2006 34: W613-W616; doi:10.1093/nar/gkl288 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fei Fang and Mathieu Blanchette

FootPrinter3: phylogenetic footprinting in partially alignable sequences
Nucl. Acids Res. 2006 34: W617-W620; doi:10.1093/nar/gkl123 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Lucía Conde, Juan M. Vaquerizas, Hernán Dopazo, Leonardo Arbiza, Joke Reumers, Frederic Rousseau, Joost Schymkowitz, and Joaquín Dopazo

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes
Nucl. Acids Res. 2006 34: W621-W625; doi:10.1093/nar/gkl071 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Purvesh Khatri, Valmik Desai, Adi L. Tarca, Sivakumar Sellamuthu, Derek E. Wildman, Roberto Romero, and Sorin Draghici

New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate
Nucl. Acids Res. 2006 34: W626-W631; doi:10.1093/nar/gkl213 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Sňnia Casillas and Antonio Barbadilla

PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA
Nucl. Acids Res. 2006 34: W632-W634; doi:10.1093/nar/gkl080 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Hsiang-Yu Yuan, Jen-Jie Chiou, Wen-Hsien Tseng, Chia-Hung Liu, Chuan-Kun Liu, Yi-Jung Lin, Hui-Hung Wang, Adam Yao, Yuan-Tsong Chen, and Chun-Nan Hsu

FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization
Nucl. Acids Res. 2006 34: W635-W641; doi:10.1093/nar/gkl236 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Areum Han, Hyo Jin Kang, Yoobok Cho, Sunghoon Lee, Young Joo Kim, and Sungsam Gong

SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences
Nucl. Acids Res. 2006 34: W642-W644; doi:10.1093/nar/gkl323 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Paul D. Thomas, Anish Kejariwal, Nan Guo, Huaiyu Mi, Michael J. Campbell, Anushya Muruganujan, and Betty Lazareva-Ulitsky

Applications for protein sequence–function evolution data: mRNA/protein expression analysis and coding SNP scoring tools
Nucl. Acids Res. 2006 34: W645-W650; doi:10.1093/nar/gkl229 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Reidar Andreson, Tarmo Puurand, and Maido Remm

SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes
Nucl. Acids Res. 2006 34: W651-W655; doi:10.1093/nar/gkl125 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Erica Jewell, Andrew Robinson, David Savage, Tim Erwin, Christopher G. Love, Geraldine A. C. Lim, Xi Li, Jacqueline Batley, German C. Spangenberg, and David Edwards

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery
Nucl. Acids Res. 2006 34: W656-W659; doi:10.1093/nar/gkl083 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Fengxia Yao, Ruifang Zhang, Zanhua Zhu, Kun Xia, and Chunyu Liu

MutScreener: primer design tool for PCR-direct sequencing
Nucl. Acids Res. 2006 34: W660-W664; doi:10.1093/nar/gkl168 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] [Request Permissions]  

Tomoyuki Yamada, Haruhiko Soma, and Shinichi Morishita

PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome
Nucl. Acids Res. 2006 34: W665-W669; doi:10.1093/nar/gkl297 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jakob Fredslund, Lene H. Madsen, Birgit K. Hougaard, Niels Sandal, Jens Stougaard, David Bertioli, and Leif Schauser

GeMprospector—online design of cross-species genetic marker candidates in legumes and grasses
Nucl. Acids Res. 2006 34: W670-W675; doi:10.1093/nar/gkl201 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Oleg Kikin, Lawrence D'Antonio, and Paramjeet S Bagga

QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences
Nucl. Acids Res. 2006 34: W676-W682; doi:10.1093/nar/gkl253 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Vinod Scaria, Manoj Hariharan, Amit Arora, and Souvik Maiti

Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences
Nucl. Acids Res. 2006 34: W683-W685; doi:10.1093/nar/gkl299 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Feng Gao and Chun-Ting Zhang

GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
Nucl. Acids Res. 2006 34: W686-W691; doi:10.1093/nar/gkl040 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Philipp W. Messer and Peter F. Arndt

CorGen—measuring and generating long-range correlations for DNA sequence analysis
Nucl. Acids Res. 2006 34: W692-W695; doi:10.1093/nar/gkl234 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Ying Chih Lin, Chin Lung Lu, Ying-Chuan Liu, and Chuan Yi Tang

SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges
Nucl. Acids Res. 2006 34: W696-W699; doi:10.1093/nar/gkl169 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

David Posada

ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online
Nucl. Acids Res. 2006 34: W700-W703; doi:10.1093/nar/gkl042 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jörg Schultz, Tobias Müller, Marco Achtziger, Philipp N. Seibel, Thomas Dandekar, and Matthias Wolf

The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses
Nucl. Acids Res. 2006 34: W704-W707; doi:10.1093/nar/gkl129 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Gábor Tóth, Gábor Deák, Endre Barta, and György B. Kiss

PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats
Nucl. Acids Res. 2006 34: W708-W713; doi:10.1093/nar/gkl263 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Luca Pireddu, Duane Szafron, Paul Lu, and Russell Greiner

The Path-A metabolic pathway prediction web server
Nucl. Acids Res. 2006 34: W714-W719; doi:10.1093/nar/gkl228 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Jianmin Wu, Xizeng Mao, Tao Cai, Jingchu Luo, and Liping Wei

KOBAS server: a web-based platform for automated annotation and pathway identification
Nucl. Acids Res. 2006 34: W720-W724; doi:10.1093/nar/gkl167 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Christopher Hyland, John W. Pinney, Glenn A. McConkey, and David R. Westhead

metaSHARK: a WWW platform for interactive exploration of metabolic networks
Nucl. Acids Res. 2006 34: W725-W728; doi:10.1093/nar/gkl196 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Duncan Hull, Katy Wolstencroft, Robert Stevens, Carole Goble, Mathew R. Pocock, Peter Li, and Tom Oinn

Taverna: a tool for building and running workflows of services
Nucl. Acids Res. 2006 34: W729-W732; doi:10.1093/nar/gkl320 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alexander Loß, Roland Stenutz, Eberhard Schwarzer, and Claus-W. von der Lieth

GlyNest and CASPER: two independent approaches to estimate ¹H and ¹³C NMR shifts of glycans available through a common web-interface
Nucl. Acids Res. 2006 34: W733-W737; doi:10.1093/nar/gkl265 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Maria A. Miteva, Stephanie Violas, Matthieu Montes, David Gomez, Pierre Tuffery, and Bruno O. Villoutreix

FAF-Drugs: free ADME/tox filtering of compound collections
Nucl. Acids Res. 2006 34: W738-W744; doi:10.1093/nar/gkl065 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Alfred D. Eaton

HubMed: a web-based biomedical literature search interface
Nucl. Acids Res. 2006 34: W745-W747; doi:10.1093/nar/gkl037 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Uma Mudunuri, Robert Stephens, David Bruining, David Liu, and Frank J. Lebeda

botXminer: mining biomedical literature with a new web-based application
Nucl. Acids Res. 2006 34: W748-W752; doi:10.1093/nar/gkl194 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]