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Previous Next 		Contents: Volume 34, Web Server issue    1 July 2006    [Index by Author] 
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Editorial:Back

EDITORIAL
Nucl. Acids Res. 2006 34: W1; doi:10.1093/nar/gkl385 [Extract] [FREE Full Text] [Print PDF][Screen PDF] [Request Permissions]  

Articles:Back

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 Tångrot, Lixiao Wang, Bo Kågström, 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 pKa 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 Stærfeldt, Peter Wad Sackett, and Anne Mølgaard
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, Håkan 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. Ferrè 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
REMUS: 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] [Supplementary Material] [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 Castrignanò, 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] [Supplementary Data] [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. Ferrè 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]