Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee (Englisch)
Freier Zugriff
- Neue Suche nach: Armougom, Fabrice
- Neue Suche nach: Moretti, Sébastien
- Neue Suche nach: Poirot, Olivier
- Neue Suche nach: Audic, Stéphane
- Neue Suche nach: Dumas, Pierre
- Neue Suche nach: Schaeli, Basile
- Neue Suche nach: Keduas, Vladimir
- Neue Suche nach: Notredame, Cedric
- Neue Suche nach: Armougom, Fabrice
- Neue Suche nach: Moretti, Sébastien
- Neue Suche nach: Poirot, Olivier
- Neue Suche nach: Audic, Stéphane
- Neue Suche nach: Dumas, Pierre
- Neue Suche nach: Schaeli, Basile
- Neue Suche nach: Keduas, Vladimir
- Neue Suche nach: Notredame, Cedric
In:
Nucleic acids research
;
34
, suppl_2
;
W604-
;
2006
- Aufsatz (Zeitschrift) / Elektronische Ressource
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Titel:Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
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Beteiligte:Armougom, Fabrice ( Autor:in ) / Moretti, Sébastien ( Autor:in ) / Poirot, Olivier ( Autor:in ) / Audic, Stéphane ( Autor:in ) / Dumas, Pierre ( Autor:in ) / Schaeli, Basile ( Autor:in ) / Keduas, Vladimir ( Autor:in ) / Notredame, Cedric ( Autor:in )
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Erschienen in:Nucleic acids research ; 34, suppl_2 ; W604-
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Verlag:
- Neue Suche nach: Oxford University Press
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Erscheinungsdatum:01.07.2006
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ISSN:
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DOI:
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Medientyp:Aufsatz (Zeitschrift)
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Format:Elektronische Ressource
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Sprache:Englisch
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Datenquelle:
Inhaltsverzeichnis – Band 34, Ausgabe suppl_2
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EDITORIAL| 2006
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A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links DirectoryFox, Joanne A. / McMillan, Scott / Ouellette, B. F. Francis et al. | 2006
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BLAST: improvements for better sequence analysisYe, Jian / McGinnis, Scott / Madden, Thomas L. et al. | 2006
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FISH--family identification of sequence homologues using structure anchored hidden Markov modelsTångrot, Jeanette / Wang, Lixiao / Kågström, Bo / Sauer, Uwe H. et al. | 2006
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The MIGenAS integrated bioinformatics toolkit for web-based sequence analysisRampp, Markus / Soddemann, Thomas / Lederer, Hermann et al. | 2006
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PreBI: prediction of biological interfaces of proteins in crystalsTsuchiya, Yuko / Kinoshita, Kengo / Ito, Nobutoshi / Nakamura, Haruki et al. | 2006
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PAST: fast structure-based searching in the PDBTäubig, Hanjo / Buchner, Arno / Griebsch, Jan et al. | 2006
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oGNM: online computation of structural dynamics using the Gaussian Network ModelYang, Lee-Wei / Rader, A. J. / Liu, Xiong / Jursa, Cristopher Jon / Chen, Shann Ching / Karimi, Hassan A. / Bahar, Ivet et al. | 2006
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PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequenceLi, Z. R. / Lin, H. H. / Han, L. Y. / Jiang, L. / Chen, X. / Chen, Y. Z. et al. | 2006
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PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostaticsAzuara, Cyril / Lindahl, Erik / Koehl, Patrice / Orland, Henri / Delarue, Marc et al. | 2006
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PHEPS: web-based pH-dependent Protein Electrostatics ServerKantardjiev, Alexander A. / Atanasov, Boris P. et al. | 2006
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pKD: re-designing protein pKa valuesTynan-Connolly, Barbara M. / Nielsen, Jens Erik et al. | 2006
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NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysisLindahl, Erik / Azuara, Cyril / Koehl, Patrice / Delarue, Marc et al. | 2006
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UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network modelsJang, Yunho / Jeong, Jay I. / Kim, Moon K. et al. | 2006
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PREDITOR: a web server for predicting protein torsion angle restraintsBerjanskii, Mark V. / Neal, Stephen / Wishart, David S. et al. | 2006
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FOLD-RATE: prediction of protein folding rates from amino acid sequenceGromiha, M. Michael / Thangakani, A. Mary / Selvaraj, S. et al. | 2006
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Protein Peeling 2: a web server to convert protein structures into series of protein unitsGelly, J.-C. / Etchebest, C. / Hazout, S. / de Brevern, A.G. et al. | 2006
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ProSAT2--Protein Structure Annotation ServerGabdoulline, R. R. / Ulbrich, S. / Richter, S. / Wade, R. C. et al. | 2006
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FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDBWernersson, Rasmus / Rapacki, Kristoffer / Stærfeldt, Hans-Henrik / Sackett, Peter Wad / Mølgaard, Anne et al. | 2006
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ProKware: integrated software for presenting protein structural properties in protein tertiary structuresHung, Jui-Hung / Huang, Hsien-Da / Lee, Tzong-Yi et al. | 2006
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OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structuresShih, Edward S. C. / Gan, Ruei-chi R. / Hwang, Ming-Jing et al. | 2006
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Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain informationLee, Sunghoon / Lee, Byungwook / Jang, Insoo / Kim, Sangsoo / Bhak, Jong et al. | 2006
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TreeDomViewer: a tool for the visualization of phylogeny and protein domain structureAlako, Blaise T. F. / Rainey, Daphne / Nijveen, Harm / Leunissen, Jack A. M. et al. | 2006
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TreeDet: a web server to explore sequence spaceCarro, Angel / Tress, Michael / de Juan, David / Pazos, Florencio / Lopez-Romero, Pedro / del Sol, Antonio / Valencia, Alfonso / Rojas, Ana M. et al. | 2006
- W116
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CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residuesDundas, Joe / Ouyang, Zheng / Tseng, Jeffery / Binkowski, Andrew / Turpaz, Yaron / Liang, Jie et al. | 2006
- W119
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Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabetTyagi, M. / Sharma, P. / Swamy, C. S. / Cadet, F. / Srinivasan, N. / de Brevern, A. G. / Offmann, B. et al. | 2006
- W124
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ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognitionAhmad, Shandar / Kono, Hidetoshi / Araúzo-Bravo, Marcos J. / Sarai, Akinori et al. | 2006
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3dSS: 3D structural superpositionSumathi, K. / Ananthalakshmi, P. / Roshan, M. N. A. Md. / Sekar, K. et al. | 2006
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MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignmentsOzer, Hatice Gulcin / Ray, William C. et al. | 2006
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HHrep: de novo protein repeat detection and the origin of TIM barrelsSöding, Johannes / Remmert, Michael / Biegert, Andreas et al. | 2006
- W143
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Cascade PSI-BLAST web server: a remote homology search tool for relating protein domainsBhadra, R. / Sandhya, S. / Abhinandan, K. R. / Chakrabarti, S. / Sowdhamini, R. / Srinivasan, N. et al. | 2006
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SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon traceMaupetit, Julien / Gautier, R. / Tufféry, Pierre et al. | 2006
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(PS)2: protein structure prediction serverChen, Chih-Chieh / Hwang, Jenn-Kang / Yang, Jinn-Moon et al. | 2006
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KemaDom: a web server for domain prediction using kernel machine with local contextChen, Lusheng / Wang, Wei / Ling, Shaoping / Jia, Caiyan / Wang, Fei et al. | 2006
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Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machinesVullo, Alessandro / Bortolami, Oscar / Pollastri, Gianluca / Tosatto, Silvio C. E. et al. | 2006
- W169
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PONGO: a web server for multiple predictions of all-alpha transmembrane proteinsAmico, Mauro / Finelli, Michele / Rossi, Ivan / Zauli, Andrea / Elofsson, Arne / Viklund, Håkan / von Heijne, Gunnar / Jones, David / Krogh, Anders / Fariselli, Piero et al. | 2006
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ArchPRED: a template based loop structure prediction serverFernandez-Fuentes, Narcis / Zhai, Jun / Fiser, András et al. | 2006
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DISULFIND: a disulfide bonding state and cysteine connectivity prediction serverCeroni, Alessio / Passerini, Andrea / Vullo, Alessandro / Frasconi, Paolo et al. | 2006
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DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classificationFerrè, F. / Clote, P. et al. | 2006
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PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteinsBigelow, Henry / Rost, Burkhard et al. | 2006
- W189
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transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrelsWaldispühl, J. / Berger, Bonnie / Clote, Peter / Steyaert, Jean-Marc et al. | 2006
- W194
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SVMHC: a server for prediction of MHC-binding peptidesDönnes, Pierre / Kohlbacher, Oliver et al. | 2006
- W198
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REMUS: a tool for identification of unique peptide segments as epitopesPai, Tun-Wen / Chang, Margaret Dah-Tsyr / Tzou, Wen-Shyong / Su, Bo-Han / Wu, Pei-Chih / Chang, Hao-Teng / Chou, Wei-I et al. | 2006
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AlgPred: prediction of allergenic proteins and mapping of IgE epitopesSaha, Sudipto / Raghava, G. P. S. et al. | 2006
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pTARGET: a web server for predicting protein subcellular localizationGuda, Chittibabu et al. | 2006
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DOUTfinder--identification of distant domain outliers using subsignificant sequence similarityNovatchkova, Maria / Schneider, Georg / Fritz, Richard / Eisenhaber, Frank / Schleiffer, Alexander et al. | 2006
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TarFisDock: a web server for identifying drug targets with docking approachLi, Honglin / Gao, Zhenting / Kang, Ling / Zhang, Hailei / Yang, Kun / Yu, Kunqian / Luo, Xiaomin / Zhu, Weiliang / Chen, Kaixian / Shen, Jianhua et al. | 2006
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sgTarget: a target selection resource for structural genomicsRodrigues, Ana P. C. / Grant, Barry J. / Hubbard, Roderick E. et al. | 2006
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HARMONY: a server for the assessment of protein structuresPugalenthi, G. / Shameer, K. / Srinivasan, N. / Sowdhamini, R. et al. | 2006
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RosettaDesign server for protein designLiu, Yi / Kuhlman, Brian et al. | 2006
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CUPSAT: prediction of protein stability upon point mutationsParthiban, Vijaya / Gromiha, M. Michael / Schomburg, Dietmar et al. | 2006
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BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequencesWang, Liangjiang / Brown, Susan J. et al. | 2006
- W249
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MeMo: a web tool for prediction of protein methylation modificationsChen, Hu / Xue, Yu / Huang, Ni / Yao, Xuebiao / Sun, Zhirong et al. | 2006
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SUMOsp: a web server for sumoylation site predictionXue, Yu / Zhou, Fengfeng / Fu, Chuanhai / Xu, Ying / Yao, Xuebiao et al. | 2006
- W258
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MODi : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectraKim, Sangtae / Na, Seungjin / Sim, Ji Woong / Park, Heejin / Jeong, Jaeho / Kim, Hokeun / Seo, Younghwan / Seo, Jawon / Lee, Kong-Joo / Paek, Eunok et al. | 2006
- W264
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DyNAVacS: an integrative tool for optimized DNA vaccine designHarish, Nagarajan / Gupta, Rekha / Agarwal, Parul / Scaria, Vinod / Pillai, Beena et al. | 2006
- W267
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NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptidesSouthey, Bruce R. / Amare, Andinet / Zimmerman, Tyler A. / Rodriguez-Zas, Sandra L. / Sweedler, Jonathan V. et al. | 2006
- W273
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BAGEL: a web-based bacteriocin genome mining toolde Jong, Anne / van Hijum, Sacha A. F. T. / Bijlsma, Jetta J. E. / Kok, Jan / Kuipers, Oscar P. et al. | 2006
- W280
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GeneAlign: a coding exon prediction tool based on phylogenetical comparisonsHsieh, Shu Ju / Lin, Chun Yuan / Liu, Ning Han / Chow, Wei Yuan / Tang, Chuan Yi et al. | 2006
- W285
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TOM: a web-based integrated approach for identification of candidate disease genesRossi, Simona / Masotti, Daniele / Nardini, Christine / Bonora, Elena / Romeo, Giovanni / Macii, Enrico / Benini, Luca / Volinia, Stefano et al. | 2006
- W293
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WEGO: a web tool for plotting GO annotationsYe, Jia / Fang, Lin / Zheng, Hongkun / Zhang, Yong / Chen, Jie / Zhang, Zengjin / Wang, Jing / Li, Shengting / Li, Ruiqiang / Bolund, Lars et al. | 2006
- W298
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APID: Agile Protein Interaction DataAnalyzerPrieto, Carlos / De Las Rivas, Javier et al. | 2006
- W303
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Protemot: prediction of protein binding sites with automatically extracted geometrical templatesChang, Darby Tien-Hao / Weng, Yi-Zhong / Lin, Jung-Hsin / Hwang, Ming-Jing / Oyang, Yen-Jen et al. | 2006
- W310
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GRAMM-X public web server for protein-protein dockingTovchigrechko, Andrey / Vakser, Ilya A. et al. | 2006
- W315
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TSEMA: interactive prediction of protein pairings between interacting familiesIzarzugaza, José M. G. / Juan, David / Pons, Carles / Ranea, Juan A. G. / Valencia, Alfonso / Pazos, Florencio et al. | 2006
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kinDOCK: a tool for comparative docking of protein kinase ligandsMartin, Laetitia / Catherinot, Vincent / Labesse, Gilles et al. | 2006
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YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology termsPenkett, Christopher J. / Morris, James A. / Wood, Valerie / Bähler, Jürg et al. | 2006
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The MPI Bioinformatics Toolkit for protein sequence analysisBiegert, Andreas / Mayer, Christian / Remmert, Michael / Söding, Johannes / Lupas, Andrei N. et al. | 2006
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VIRGO: computational prediction of gene functionsMassjouni, Naveed / Rivera, Corban G. / Murali, T. M. et al. | 2006
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TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDBYamasaki, Chisato / Kawashima, Hiroaki / Todokoro, Fusano / Imamizu, Yasuhiro / Ogawa, Makoto / Tanino, Motohiko / Itoh, Takeshi / Gojobori, Takashi / Imanishi, Tadashi et al. | 2006
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DILIMOT: discovery of linear motifs in proteinsNeduva, Victor / Russell, Robert B. et al. | 2006
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MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequencesHsu, Chen-Ming / Chen, Chien-Yu / Liu, Baw-Jhiune et al. | 2006
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ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteinsde Castro, Edouard / Sigrist, Christian J. A. / Gattiker, Alexandre / Bulliard, Virginie / Langendijk-Genevaux, Petra S. / Gasteiger, Elisabeth / Bairoch, Amos / Hulo, Nicolas et al. | 2006
- W366
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MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomesNeph, Shane / Tompa, Martin et al. | 2006
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MEME: discovering and analyzing DNA and protein sequence motifsBailey, Timothy L. / Williams, Nadya / Misleh, Chris / Li, Wilfred W. et al. | 2006
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HHsenser: exhaustive transitive profile search using HMM-HMM comparisonSöding, Johannes / Remmert, Michael / Biegert, Andreas / Lupas, Andrei N. et al. | 2006
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JAFA: a protein function annotation meta-serverFriedberg, Iddo / Harder, Tim / Godzik, Adam et al. | 2006
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SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysisLiang, Han / Zhou, Weihua / Landweber, Laura F. et al. | 2006
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Virtual Ribosome--a comprehensive DNA translation tool with support for integration of sequence feature annotationWernersson, Rasmus et al. | 2006
- W389
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GenDecoder: genetic code prediction for metazoan mitochondriaAbascal, Federico / Zardoya, Rafael / Posada, David et al. | 2006
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NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genesDeSantis, T. Z. / Hugenholtz, P. / Keller, K. / Brodie, E. L. / Larsen, N. / Piceno, Y. M. / Phan, R. / Andersen, G. L. et al. | 2006
- W400
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CrossLink: visualization and exploration of sequence relationships between (micro) RNAsDezulian, Tobias / Schaefer, Martin / Wiese, Roland / Weigel, Detlef / Huson, Daniel H. et al. | 2006
- W405
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CorreLogo: an online server for 3D sequence logos of RNA and DNA alignmentsBindewald, Eckart / Schneider, Thomas D. / Shapiro, Bruce A. et al. | 2006
- W412
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The ARTS web server for aligning RNA tertiary structuresDror, Oranit / Nussinov, Ruth / Wolfson, Haim J. et al. | 2006
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PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structuresByun, Yanga / Han, Kyungsook et al. | 2006
- W423
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RNAMST: efficient and flexible approach for identifying RNA structural homologsChang, Tzu-Hao / Huang, Hsien-Da / Chuang, Tzu-Neng / Shien, Dray-Ming / Horng, Jorng-Tzong et al. | 2006
- W429
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RegRNA: an integrated web server for identifying regulatory RNA motifs and elementsHuang, Hsi-Yuan / Chien, Chia-Hung / Jen, Kuan-Hua / Huang, Hsien-Da et al. | 2006
- W435
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AUGUSTUS: ab initio prediction of alternative transcriptsStanke, Mario / Keller, Oliver / Gunduz, Irfan / Hayes, Alec / Waack, Stephan / Morgenstern, Burkhard et al. | 2006
- W440
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ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterizationCastrignanò, Tiziana / Rizzi, Raffaella / Talamo, Ivano Giuseppe / De Meo, Paolo D'Onorio / Anselmo, Anna / Bonizzoni, Paola / Pesole, Graziano et al. | 2006
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ASGS: an alternative splicing graph web serviceBollina, Durgaprasad / Lee, Bernett T. K. / Tan, Tin Wee / Ranganathan, Shoba et al. | 2006
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siVirus: web-based antiviral siRNA design software for highly divergent viral sequencesNaito, Yuki / Ui-Tei, Kumiko / Nishikawa, Toru / Takebe, Yutaka / Saigo, Kaoru et al. | 2006
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RNAhybrid: microRNA target prediction easy, fast and flexibleKrüger, Jan / Rehmsmeier, Marc et al. | 2006
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ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAsNam, Jin-Wu / Kim, Jinhan / Kim, Sung-Kyu / Zhang, Byoung-Tak et al. | 2006
- W459
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EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragmentsMasoudi-Nejad, Ali / Tonomura, Koichiro / Kawashima, Shuichi / Moriya, Yuki / Suzuki, Masanori / Itoh, Masumi / Kanehisa, Minoru / Endo, Takashi / Goto, Susumu et al. | 2006
- W463
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jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1Zhang, Ming / Schultz, Anne-Kathrin / Calef, Charles / Kuiken, Carla / Leitner, Thomas / Korber, Bette / Morgenstern, Burkhard / Stanke, Mario et al. | 2006
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BiologicalNetworks: visualization and analysis tool for systems biologyBaitaluk, Michael / Sedova, Mayya / Ray, Animesh / Gupta, Amarnath et al. | 2006
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BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experimentsAl-Shahrour, Fátima / Minguez, Pablo / Tárraga, Joaquín / Montaner, David / Alloza, Eva / Vaquerizas, Juan M. / Conde, Lucía / Blaschke, Christian / Vera, Javier / Dopazo, Joaquín et al. | 2006
- W477
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CAPweb: a bioinformatics CGH array Analysis PlatformLiva, Stéphane / Hupé, Philippe / Neuvial, Pierre / Brito, Isabel / Viara, Eric / Rosa, Philippe La / Barillot, Emmanuel et al. | 2006
- W482
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BTW: a web server for Boltzmann time warping of gene expression time seriesFerrè, F. / Clote, P. et al. | 2006
- W486
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Next station in microarray data analysis: GEPASMontaner, David / Tárraga, Joaquín / Huerta-Cepas, Jaime / Burguet, Jordi / Vaquerizas, Juan M. / Conde, Lucía / Minguez, Pablo / Vera, Javier / Mukherjee, Sach / Valls, Joan et al. | 2006
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GEPS: the Gene Expression Pattern ScannerWang, Yu-Peng / Liang, Liang / Han, Bu-Cong / Quan, Yu / Wang, Xiao / Tao, Tao / Ji, Zhi-Liang et al. | 2006
- W498
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CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysisRainer, Johannes / Sanchez-Cabo, Fatima / Stocker, Gernot / Sturn, Alexander / Trajanoski, Zlatko et al. | 2006
- W504
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Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysisManfield, Iain W. / Jen, Chih-Hung / Pinney, John W. / Michalopoulos, Ioannis / Bradford, James R. / Gilmartin, Philip M. / Westhead, David R. et al. | 2006
- W510
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JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology informationScheer, Maurice / Klawonn, Frank / Münch, Richard / Grote, Andreas / Hiller, Karsten / Choi, Claudia / Koch, Ina / Schobert, Max / Härtig, Elisabeth / Klages, Ulrich et al. | 2006
- W516
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Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleasesMandell, Jeffrey G. / Barbas, Carlos F. et al. | 2006
- W524
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TFBScluster web server for the identification of mammalian composite regulatory elementsDonaldson, Ian J. / Göttgens, Berthold et al. | 2006
- W529
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VOMBAT: prediction of transcription factor binding sites using variable order Bayesian treesGrau, Jan / Ben-Gal, Irad / Posch, Stefan / Grosse, Ivo et al. | 2006
- W534
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POXO: a web-enabled tool series to discover transcription factor binding sitesKankainen, Matti / Pehkonen, Petri / Rosenstöm, Päivi / Törönen, Petri / Wong, Garry / Holm, Liisa et al. | 2006
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Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithmWaleev, T. / Shtokalo, D. / Konovalova, T. / Voss, N. / Cheremushkin, E. / Stegmaier, P. / Kel-Margoulis, O. / Wingender, E. / Kel, A. et al. | 2006
- W546
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jPREdictor: a versatile tool for the prediction of cis-regulatory elementsFiedler, Thomas / Rehmsmeier, Marc et al. | 2006
- W551
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CEAS: cis-regulatory element annotation systemJi, Xuwo / Li, Wei / Song, Jun / Wei, Liping / Liu, X. Shirley et al. | 2006
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Stubb: a program for discovery and analysis of cis-regulatory modulesSinha, Saurabh / Liang, Yupu / Siggia, Eric et al. | 2006
- W560
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NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factorsLuykx, Peter / Bajic, Ivan V. / Khuri, Sawsan et al. | 2006
- W566
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MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genesPavesi, Giulio / Mereghetti, Paolo / Zambelli, Federico / Stefani, Marco / Mauri, Giancarlo / Pesole, Graziano et al. | 2006
- W571
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CRSD: a comprehensive web server for composite regulatory signature discoveryLiu, Chun-Chi / Lin, Chin-Chung / Chen, Wen-Shyen E. / Chen, Hsuan-Yu / Chang, Pei-Chun / Chen, Jeremy J.W. / Yang, Pan-Chyr et al. | 2006
- W578
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PromAn: an integrated knowledge-based web server dedicated to promoter analysisLardenois, Aurélie / Chalmel, Frédéric / Bianchetti, Laurent / Sahel, José-Alain / Léveillard, Thierry / Poch, Olivier et al. | 2006
- W584
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iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic speciesRanjan, Sarita / Seshadri, Jayshree / Vindal, Vaibhav / Yellaboina, Sailu / Ranjan, Akash et al. | 2006
- W588
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TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sitesTech, M. / Morgenstern, B. / Meinicke, P. et al. | 2006
- W591
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FeatureScan: revealing property-dependent similarity of nucleotide sequencesDeyneko, Igor V. / Bredohl, Björn / Wesely, Daniel / Kalybaeva, Yulia M. / Kel, Alexander E. / Blöcker, Helmut / Kauer, Gerhard et al. | 2006
- W596
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Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignmentLassmann, Timo / Sonnhammer, Erik L. L. et al. | 2006
- W600
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PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignmentsMoretti, Sébastien / Reinier, Frédéric / Poirot, Olivier / Armougom, Fabrice / Audic, Stéphane / Keduas, Vladimir / Notredame, Cédric et al. | 2006
- W604
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Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-CoffeeArmougom, Fabrice / Moretti, Sébastien / Poirot, Olivier / Audic, Stéphane / Dumas, Pierre / Schaeli, Basile / Keduas, Vladimir / Notredame, Cedric et al. | 2006
- W609
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PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignmentsSuyama, Mikita / Torrents, David / Bork, Peer et al. | 2006
- W613
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AliWABA: alignment on the web through an A-Bruijn approachJones, Neil C. / Zhi, Degui / Raphael, Benjamin J. et al. | 2006
- W617
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FootPrinter3: phylogenetic footprinting in partially alignable sequencesFang, Fei / Blanchette, Mathieu et al. | 2006
- W621
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PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposesConde, Lucía / Vaquerizas, Juan M. / Dopazo, Hernán / Arbiza, Leonardo / Reumers, Joke / Rousseau, Frederic / Schymkowitz, Joost / Dopazo, Joaquín et al. | 2006
- W626
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New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-TranslateKhatri, Purvesh / Desai, Valmik / Tarca, Adi L. / Sellamuthu, Sivakumar / Wildman, Derek E. / Romero, Roberto / Draghici, Sorin et al. | 2006
- W632
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PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNACasillas, Sònia / Barbadilla, Antonio et al. | 2006
- W635
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FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritizationYuan, Hsiang-Yu / Chiou, Jen-Jie / Tseng, Wen-Hsien / Liu, Chia-Hung / Liu, Chuan-Kun / Lin, Yi-Jung / Wang, Hui-Hung / Yao, Adam / Chen, Yuan-Tsong / Hsu, Chun-Nan et al. | 2006
- W642
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SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequencesHan, Areum / Kang, Hyo Jin / Cho, Yoobok / Lee, Sunghoon / Kim, Young Joo / Gong, Sungsam et al. | 2006
- W645
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Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring toolsThomas, Paul D. / Kejariwal, Anish / Guo, Nan / Mi, Huaiyu / Campbell, Michael J. / Muruganujan, Anushya / Lazareva-Ulitsky, Betty et al. | 2006
- W651
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SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomesAndreson, Reidar / Puurand, Tarmo / Remm, Maido et al. | 2006
- W656
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SSRPrimer and SSR Taxonomy Tree: Biome SSR discoveryJewell, Erica / Robinson, Andrew / Savage, David / Erwin, Tim / Love, Christopher G. / Lim, Geraldine A. C. / Li, Xi / Batley, Jacqueline / Spangenberg, German C. / Edwards, David et al. | 2006
- W660
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MutScreener: primer design tool for PCR-direct sequencingYao, Fengxia / Zhang, Ruifang / Zhu, Zanhua / Xia, Kun / Liu, Chunyu et al. | 2006
- W665
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PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genomeYamada, Tomoyuki / Soma, Haruhiko / Morishita, Shinichi et al. | 2006
- W670
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GeMprospector--online design of cross-species genetic marker candidates in legumes and grassesFredslund, Jakob / Madsen, Lene H. / Hougaard, Birgit K. / Sandal, Niels / Stougaard, Jens / Bertioli, David / Schauser, Leif et al. | 2006
- W676
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QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequencesKikin, Oleg / D'Antonio, Lawrence / Bagga, Paramjeet S et al. | 2006
- W683
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Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequencesScaria, Vinod / Hariharan, Manoj / Arora, Amit / Maiti, Souvik et al. | 2006
- W686
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GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequencesGao, Feng / Zhang, Chun-Ting et al. | 2006
- W692
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CorGen--measuring and generating long-range correlations for DNA sequence analysisMesser, Philipp W. / Arndt, Peter F. et al. | 2006
- W696
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SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchangesLin, Ying Chih / Lu, Chin Lung / Liu, Ying-Chuan / Tang, Chuan Yi et al. | 2006
- W700
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ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution onlinePosada, David et al. | 2006
- W704
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The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analysesSchultz, Jörg / Müller, Tobias / Achtziger, Marco / Seibel, Philipp N. / Dandekar, Thomas / Wolf, Matthias et al. | 2006
- W708
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PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeatsTóth, Gábor / Deák, Gábor / Barta, Endre / Kiss, György B. et al. | 2006
- W714
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The Path-A metabolic pathway prediction web serverPireddu, Luca / Szafron, Duane / Lu, Paul / Greiner, Russell et al. | 2006
- W720
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KOBAS server: a web-based platform for automated annotation and pathway identificationWu, Jianmin / Mao, Xizeng / Cai, Tao / Luo, Jingchu / Wei, Liping et al. | 2006
- W725
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metaSHARK: a WWW platform for interactive exploration of metabolic networksHyland, Christopher / Pinney, John W. / McConkey, Glenn A. / Westhead, David R. et al. | 2006
- W729
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Taverna: a tool for building and running workflows of servicesHull, Duncan / Wolstencroft, Katy / Stevens, Robert / Goble, Carole / Pocock, Mathew R. / Li, Peter / Oinn, Tom et al. | 2006
- W733
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GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interfaceLoß, Alexander / Stenutz, Roland / Schwarzer, Eberhard / von der Lieth, Claus-W. et al. | 2006
- W738
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FAF-Drugs: free ADME/tox filtering of compound collectionsMiteva, Maria A. / Violas, Stephanie / Montes, Matthieu / Gomez, David / Tuffery, Pierre / Villoutreix, Bruno O. et al. | 2006
- W745
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HubMed: a web-based biomedical literature search interfaceEaton, Alfred D. et al. | 2006
- W748
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botXminer: mining biomedical literature with a new web-based applicationMudunuri, Uma / Stephens, Robert / Bruining, David / Liu, David / Lebeda, Frank J. et al. | 2006