Nucl. Acids Res. -- Table of Contents (33 [Web Server Issue])

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Contents: Volume 33, Web Server Issue    July 1 2005    [Index by Author]

       Editorial

       Articles

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Editorial:

: EDITORIAL
Nucl. Acids Res. 2005 33: W1; doi:10.1093/nar/gki592 [Extract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Articles:

Joanne A. Fox, Stefanie L. Butland, Scott McMillan, Graeme Campbell, and B. F. Francis Ouellette: The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers
Nucl. Acids Res. 2005 33: W3-W24; doi:10.1093/nar/gki594 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

S. Pillai, V. Silventoinen, K. Kallio, M. Senger, S. Sobhany, J. Tate, S. Velankar, A. Golovin, K. Henrick, P. Rice, P. Stoehr, and R. Lopez: SOAP-based services provided by the European Bioinformatics Institute
Nucl. Acids Res. 2005 33: W25-W28; doi:10.1093/nar/gki491 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Goran Neshich, Luiz C. Borro, Roberto H. Higa, Paula R. Kuser, Michel E. B. Yamagishi, Eduardo H. Franco, Joao N. Krauchenco, Renato Fileto, André A. Ribeiro, George B. P. Bezerra, Thiago M. Velludo, Tomás S. Jimenez, Noboru Furukawa, Hirofumi Teshima, Koji Kitajima, Abdulla Bava, Akinori Sarai, Roberto C. Togawa, and Adauto L. Mancini: The Diamond STING server
Nucl. Acids Res. 2005 33: W29-W35; doi:10.1093/nar/gki397 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Kevin Bryson, Liam J. McGuffin, Russell L. Marsden, Jonathan J. Ward, Jaspreet S. Sodhi, and David T. Jones: Protein structure prediction servers at University College London
Nucl. Acids Res. 2005 33: W36-W38; doi:10.1093/nar/gki410 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Vladimir Sobolev, Eran Eyal, Sergey Gerzon, Vladimir Potapov, Mariana Babor, Jaime Prilusky, and Marvin Edelman: SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment
Nucl. Acids Res. 2005 33: W39-W43; doi:10.1093/nar/gki398 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

C. Alland, F. Moreews, D. Boens, M. Carpentier, S. Chiusa, M. Lonquety, N. Renault, Y. Wong, H. Cantalloube, J. Chomilier, J. Hochez, J. Pothier, B. O. Villoutreix, J.-F. Zagury, and P. Tufféry: RPBS: a web resource for structural bioinformatics
Nucl. Acids Res. 2005 33: W44-W49; doi:10.1093/nar/gki477 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Alessandro Paiardini, Francesco Bossa, and Stefano Pascarella: CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology
Nucl. Acids Res. 2005 33: W50-W55; doi:10.1093/nar/gki416 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Gabriela G. Loots and Ivan Ovcharenko: Dcode.org anthology of comparative genomic tools
Nucl. Acids Res. 2005 33: W56-W64; doi:10.1093/nar/gki355 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Jérôme Gracy and Laurent Chiche: PAT: a protein analysis toolkit for integrated biocomputing on the web
Nucl. Acids Res. 2005 33: W65-W71; doi:10.1093/nar/gki455 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material][Supplementary Material] OPEN ACCESS ARTICLE

J. Cheng, A. Z. Randall, M. J. Sweredoski, and P. Baldi: SCRATCH: a protein structure and structural feature prediction server
Nucl. Acids Res. 2005 33: W72-W76; doi:10.1093/nar/gki396 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Ling-Hong Hung, Shing-Chung Ngan, Tianyun Liu, and Ram Samudrala: PROTINFO: new algorithms for enhanced protein structure predictions
Nucl. Acids Res. 2005 33: W77-W80; doi:10.1093/nar/gki403 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Ori Sasson and Michal Linial: ProTarget: automatic prediction of protein structure novelty
Nucl. Acids Res. 2005 33: W81-W84; doi:10.1093/nar/gki389 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

P. Ananthalakshmi, Ch. Kiran Kumar, M. Jeyasimhan, K. Sumathi, and K. Sekar: Fragment Finder: a web-based software to identify similar three-dimensional structural motif
Nucl. Acids Res. 2005 33: W85-W88; doi:10.1093/nar/gki353 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Roman A. Laskowski, James D. Watson, and Janet M. Thornton: ProFunc: a server for predicting protein function from 3D structure
Nucl. Acids Res. 2005 33: W89-W93; doi:10.1093/nar/gki414 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Guoli Wang and Roland L. Dunbrack, Jr: PISCES: recent improvements to a PDB sequence culling server
Nucl. Acids Res. 2005 33: W94-W98; doi:10.1093/nar/gki402 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Vladimir A. Ivanisenko, Alexey M. Eroshkin, and Nickolay A. Kolchanov: WebProAnalyst: an interactive tool for analysis of quantitative structure–activity relationships in protein families
Nucl. Acids Res. 2005 33: W99-W104; doi:10.1093/nar/gki421 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Dan Xie, Ao Li, Minghui Wang, Zhewen Fan, and Huanqing Feng: LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST
Nucl. Acids Res. 2005 33: W105-W110; doi:10.1093/nar/gki359 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

A. Zemla, C. Ecale Zhou, T. Slezak, T. Kuczmarski, D. Rama, C. Torres, D. Sawicka, and D. Barsky: AS2TS system for protein structure modeling and analysis
Nucl. Acids Res. 2005 33: W111-W115; doi:10.1093/nar/gki457 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

E. Quevillon, V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, and R. Lopez: InterProScan: protein domains identifier
Nucl. Acids Res. 2005 33: W116-W120; doi:10.1093/nar/gki442 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Maria Novatchkova, Michael Wildpaner, Dieter Schweizer, and Frank Eisenhaber: PhyloDome—visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets
Nucl. Acids Res. 2005 33: W121-W125; doi:10.1093/nar/gki373 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

O. Krishnadev, N. Rekha, S. B. Pandit, S. Abhiman, S. Mohanty, L. S. Swapna, S. Gore, and N. Srinivasan: PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families
Nucl. Acids Res. 2005 33: W126-W129; doi:10.1093/nar/gki474 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Ganesan Pugalenthi, Govindaraju Archunan, and Ramanathan Sowdhamini: DIAL: a web-based server for the automatic identification of structural domains in proteins
Nucl. Acids Res. 2005 33: W130-W132; doi:10.1093/nar/gki427 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, and Manuela Helmer-Citterich: pdbFun: mass selection and fast comparison of annotated PDB residues
Nucl. Acids Res. 2005 33: W133-W137; doi:10.1093/nar/gki499 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Pedro A. Reche and Ellis L. Reinherz: PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands
Nucl. Acids Res. 2005 33: W138-W142; doi:10.1093/nar/gki357 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Manoj Bhasin and G. P. S. Raghava: GPCRsclass: a web tool for the classification of amine type of G-protein-coupled receptors
Nucl. Acids Res. 2005 33: W143-W147; doi:10.1093/nar/gki351 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Yukimitsu Yabuki, Takahiko Muramatsu, Takatsugu Hirokawa, Hidehito Mukai, and Makiko Suwa: GRIFFIN: a system for predicting GPCR–G-protein coupling selectivity using a support vector machine and a hidden Markov model
Nucl. Acids Res. 2005 33: W148-W153; doi:10.1093/nar/gki495 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Manish Kumar, Manoj Bhasin, Navjot K. Natt, and G. P. S. Raghava: BhairPred: prediction of ß-hairpins in a protein from multiple alignment information using ANN and SVM techniques
Nucl. Acids Res. 2005 33: W154-W159; doi:10.1093/nar/gki588 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Richard A. George, Kuang Lin, and Jaap Heringa: Scooby-domain: prediction of globular domains in protein sequence
Nucl. Acids Res. 2005 33: W160-W163; doi:10.1093/nar/gki381 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

M. Michael Gromiha, Shandar Ahmad, and Makiko Suwa: TMBETA-NET: discrimination and prediction of membrane spanning ß-strands in outer membrane proteins
Nucl. Acids Res. 2005 33: W164-W167; doi:10.1093/nar/gki367 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Urmila Kulkarni-Kale, Shriram Bhosle, and A. S. Kolaskar: CEP: a conformational epitope prediction server
Nucl. Acids Res. 2005 33: W168-W171; doi:10.1093/nar/gki460 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Guang Lan Zhang, Asif M. Khan, Kellathur N. Srinivasan, J. Thomas August, and Vladimir Brusic: MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides
Nucl. Acids Res. 2005 33: W172-W179; doi:10.1093/nar/gki452 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Guang Lan Zhang, Kellathur N. Srinivasan, Anitha Veeramani, J. Thomas August, and Vladimir Brusic: PRED^BALB/c: a system for the prediction of peptide binding to H2^d molecules, a haplotype of the BALB/c mouse
Nucl. Acids Res. 2005 33: W180-W183; doi:10.1093/nar/gki479 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Yu Xue, Fengfeng Zhou, Minjie Zhu, Kashif Ahmed, Guoliang Chen, and Xuebiao Yao: GPS: a comprehensive www server for phosphorylation sites prediction
Nucl. Acids Res. 2005 33: W184-W187; doi:10.1093/nar/gki393 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Andrew G. Garrow, Alison Agnew, and David R. Westhead: TMB-Hunt: a web server to screen sequence sets for transmembrane ß-barrel proteins
Nucl. Acids Res. 2005 33: W188-W192; doi:10.1093/nar/gki384 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Hongyi Zhou, Chi Zhang, Song Liu, and Yaoqi Zhou: Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations
Nucl. Acids Res. 2005 33: W193-W197; doi:10.1093/nar/gki360 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Piero Fariselli, Michele Finelli, Ivan Rossi, Mauro Amico, Andrea Zauli, Pier Luigi Martelli, and Rita Casadio: TRAMPLE: the transmembrane protein labelling environment
Nucl. Acids Res. 2005 33: W198-W201; doi:10.1093/nar/gki440 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Manoj Bhasin and G. P. S. Raghava: Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences
Nucl. Acids Res. 2005 33: W202-W207; doi:10.1093/nar/gki587 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Christina Backes, Jan Kuentzer, Hans-Peter Lenhof, Nicole Comtesse, and Eckart Meese: GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences
Nucl. Acids Res. 2005 33: W208-W213; doi:10.1093/nar/gki433 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Andreas Bohne-Lang and Claus-Wilhelm von der Lieth: GlyProt: in silico glycosylation of proteins
Nucl. Acids Res. 2005 33: W214-W219; doi:10.1093/nar/gki385 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Pankaj Kamra, Rajesh S. Gokhale, and Debasisa Mohanty: SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites
Nucl. Acids Res. 2005 33: W220-W225; doi:10.1093/nar/gki449 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, and Jorng-Tzong Horng: KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites
Nucl. Acids Res. 2005 33: W226-W229; doi:10.1093/nar/gki471 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

F. Ferrè and P. Clote: DiANNA: a web server for disulfide connectivity prediction
Nucl. Acids Res. 2005 33: W230-W232; doi:10.1093/nar/gki412 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Darby Tien-Hau Chang, Yen-Jen Oyang, and Jung-Hsin Lin: MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm
Nucl. Acids Res. 2005 33: W233-W238; doi:10.1093/nar/gki586 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Markus Gruber, Johannes Söding, and Andrei N. Lupas: REPPER—repeats and their periodicities in fibrous proteins
Nucl. Acids Res. 2005 33: W239-W243; doi:10.1093/nar/gki405 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Johannes Söding, Andreas Biegert, and Andrei N. Lupas: The HHpred interactive server for protein homology detection and structure prediction
Nucl. Acids Res. 2005 33: W244-W248; doi:10.1093/nar/gki408 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Iddo Friedberg and Adam Godzik: Fragnostic: walking through protein structure space
Nucl. Acids Res. 2005 33: W249-W251; doi:10.1093/nar/gki363 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Kristian Vlahovicek, Alessandro Pintar, Laavanya Parthasarathi, Oliviero Carugo, and Sándor Pongor: CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures
Nucl. Acids Res. 2005 33: W252-W254; doi:10.1093/nar/gki362 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Roee Gutman, Carine Berezin, Roy Wollman, Yossi Rosenberg, and Nir Ben-Tal: QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns
Nucl. Acids Res. 2005 33: W255-W261; doi:10.1093/nar/gki496 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Thomas Yan, Danny Yoo, Tanya Z. Berardini, Lukas A. Mueller, Dan C. Weems, Shuai Weng, J. Michael Cherry, and Seung Y. Rhee: PatMatch: a program for finding patterns in peptide and nucleotide sequences
Nucl. Acids Res. 2005 33: W262-W266; doi:10.1093/nar/gki368 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

David La and Dennis R. Livesay: MINER: software for phylogenetic motif identification
Nucl. Acids Res. 2005 33: W267-W270; doi:10.1093/nar/gki465 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

S. Roepcke, P. Fiziev, P. H. Seeburg, and M. Vingron: SVC: structured visualization of evolutionary sequence conservation
Nucl. Acids Res. 2005 33: W271-W273; doi:10.1093/nar/gki589 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Saikat Chakrabarti, A. Prem Anand, Nitin Bhardwaj, Ganesan Pugalenthi, and R. Sowdhamini: SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs
Nucl. Acids Res. 2005 33: W274-W276; doi:10.1093/nar/gki493 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Iris Bahir and Michal Linial: ProTeus: identifying signatures in protein termini
Nucl. Acids Res. 2005 33: W277-W280; doi:10.1093/nar/gki371 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Milana Frenkel-Morgenstern, Alice Singer, Hagit Bronfeld, and Shmuel Pietrokovski: One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries
Nucl. Acids Res. 2005 33: W281-W283; doi:10.1093/nar/gki488 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Lukasz Jaroszewski, Leszek Rychlewski, Zhanwen Li, Weizhong Li, and Adam Godzik: FFAS03: a server for profile–profile sequence alignments
Nucl. Acids Res. 2005 33: W284-W288; doi:10.1093/nar/gki418 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

V. A. Simossis and J. Heringa: PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
Nucl. Acids Res. 2005 33: W289-W294; doi:10.1093/nar/gki390 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Can Alkan, Eray Tüzün, Jerome Buard, Franck Lethiec, Evan E. Eichler, Jeffrey A. Bailey, and S. Cenk Sahinalp: Manipulating multiple sequence alignments via MaM and WebMaM
Nucl. Acids Res. 2005 33: W295-W298; doi:10.1093/nar/gki406 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Meytal Landau, Itay Mayrose, Yossi Rosenberg, Fabian Glaser, Eric Martz, Tal Pupko, and Nir Ben-Tal: ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
Nucl. Acids Res. 2005 33: W299-W302; doi:10.1093/nar/gki370 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Csaba Magyar, M. Michael Gromiha, Gerard Pujadas, Gábor E. Tusnády, and István Simon: SRide: a server for identifying stabilizing residues in proteins
Nucl. Acids Res. 2005 33: W303-W305; doi:10.1093/nar/gki409 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Emidio Capriotti, Piero Fariselli, and Rita Casadio: I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
Nucl. Acids Res. 2005 33: W306-W310; doi:10.1093/nar/gki375 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Jessica Dantzer, Charles Moad, Randy Heiland, and Sean Mooney: MutDB services: interactive structural analysis of mutation data
Nucl. Acids Res. 2005 33: W311-W314; doi:10.1093/nar/gki404 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

William C. Ray: MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features
Nucl. Acids Res. 2005 33: W315-W319; doi:10.1093/nar/gki374 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Cédric Binisti, Ahmed Ali Salim, and Pierre Tufféry: PPG: online generation of protein pictures and animations
Nucl. Acids Res. 2005 33: W320-W323; doi:10.1093/nar/gki392 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Jason McDermott, Michal Guerquin, Zach Frazier, Aaron N. Chang, and Ram Samudrala: BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes
Nucl. Acids Res. 2005 33: W324-W325; doi:10.1093/nar/gki401 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Didier Croes, Fabian Couche, Shoshana J. Wodak, and Jacques van Helden: Metabolic PathFinding: inferring relevant pathways in biochemical networks
Nucl. Acids Res. 2005 33: W326-W330; doi:10.1093/nar/gki437 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Utkan Ogmen, Ozlem Keskin, A. Selim Aytuna, Ruth Nussinov, and Attila Gursoy: PRISM: protein interactions by structural matching
Nucl. Acids Res. 2005 33: W331-W336; doi:10.1093/nar/gki585 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Alexandra Shulman-Peleg, Ruth Nussinov, and Haim J. Wolfson: SiteEngines: recognition and comparison of binding sites and protein–protein interfaces
Nucl. Acids Res. 2005 33: W337-W341; doi:10.1093/nar/gki482 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Jens Kleinjung and Franca Fraternali: POPSCOMP: an automated interaction analysis of biomolecular complexes
Nucl. Acids Res. 2005 33: W342-W346; doi:10.1093/nar/gki369 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost, and Alfonso Valencia: EVAcon: a protein contact prediction evaluation service
Nucl. Acids Res. 2005 33: W347-W351; doi:10.1093/nar/gki411 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Zhenjun Hu, Joe Mellor, Jie Wu, Takuji Yamada, Dustin Holloway, and Charles DeLisi: VisANT: data-integrating visual framework for biological networks and modules
Nucl. Acids Res. 2005 33: W352-W357; doi:10.1093/nar/gki431 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Rajarshi Maiti, Gary H. Van Domselaar, and David S. Wishart: MovieMaker: a web server for rapid rendering of protein motions and interactions
Nucl. Acids Res. 2005 33: W358-W362; doi:10.1093/nar/gki485 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, and Haim J. Wolfson: PatchDock and SymmDock: servers for rigid and symmetric docking
Nucl. Acids Res. 2005 33: W363-W367; doi:10.1093/nar/gki481 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

John C. Gordon, Jonathan B. Myers, Timothy Folta, Valia Shoja, Lenwood S. Heath, and Alexey Onufriev: H++: a server for estimating pK_as and adding missing hydrogens to macromolecules
Nucl. Acids Res. 2005 33: W368-W371; doi:10.1093/nar/gki464 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Maria A. Miteva, Pierre Tufféry, and Bruno O. Villoutreix: PCE: web tools to compute protein continuum electrostatics
Nucl. Acids Res. 2005 33: W372-W375; doi:10.1093/nar/gki365 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Brian D. Halligan, Victor Ruotti, Simon N. Twigger, and Andrew S. Greene: DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy
Nucl. Acids Res. 2005 33: W376-W381; doi:10.1093/nar/gki461 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, and Luis Serrano: The FoldX web server: an online force field
Nucl. Acids Res. 2005 33: W382-W388; doi:10.1093/nar/gki387 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Christopher T. Workman, Yutong Yin, David L. Corcoran, Trey Ideker, Gary D. Stormo, and Panayiotis V. Benos: enoLOGOS: a versatile web tool for energy normalized sequence logos
Nucl. Acids Res. 2005 33: W389-W392; doi:10.1093/nar/gki439 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Stein Aerts, Peter Van Loo, Gert Thijs, Herbert Mayer, Rainer de Martin, Yves Moreau, and Bart De Moor: TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis
Nucl. Acids Res. 2005 33: W393-W396; doi:10.1093/nar/gki354 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Nils Ole Steffens, Claudia Galuschka, Martin Schindler, Lorenz Bülow, and Reinhard Hehl: AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana
Nucl. Acids Res. 2005 33: W397-W402; doi:10.1093/nar/gki395 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Ivan Ovcharenko and Marcelo A. Nobrega: Identifying synonymous regulatory elements in vertebrate genomes
Nucl. Acids Res. 2005 33: W403-W407; doi:10.1093/nar/gki466 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Anil G. Jegga, Ashima Gupta, Sivakumar Gowrisankar, Mrunal A. Deshmukh, Steven Connolly, Kevin Finley, and Bruce J. Aronow: CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes
Nucl. Acids Res. 2005 33: W408-W411; doi:10.1093/nar/gki486 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Guandong Wang, Taotao Yu, and Weixiong Zhang: WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar
Nucl. Acids Res. 2005 33: W412-W416; doi:10.1093/nar/gki492 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Oleg V. Vishnevsky and Nikolay A. Kolchanov: ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters
Nucl. Acids Res. 2005 33: W417-W422; doi:10.1093/nar/gki459 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Alessandro Di Cara, Karsten Schmidt, Brian A. Hemmings, and Edward J. Oakeley: PromoterPlot: a graphical display of promoter similarities by pattern recognition
Nucl. Acids Res. 2005 33: W423-W426; doi:10.1093/nar/gki413 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Matti Kankainen and Liisa Holm: POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets
Nucl. Acids Res. 2005 33: W427-W431; doi:10.1093/nar/gki467 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

D. S. Chekmenev, C. Haid, and A. E. Kel: P-Match: transcription factor binding site search by combining patterns and weight matrices
Nucl. Acids Res. 2005 33: W432-W437; doi:10.1093/nar/gki441 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Stefan Roepcke, Steffen Grossmann, Sven Rahmann, and Martin Vingron: T-Reg Comparator: an analysis tool for the comparison of position weight matrices
Nucl. Acids Res. 2005 33: W438-W441; doi:10.1093/nar/gki590 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

David L. Corcoran, Eleanor Feingold, and Panayiotis V. Benos: FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
Nucl. Acids Res. 2005 33: W442-W446; doi:10.1093/nar/gki420 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Eugene Berezikov, Victor Guryev, and Edwin Cuppen: CONREAL web server: identification and visualization of conserved transcription factor binding sites
Nucl. Acids Res. 2005 33: W447-W450; doi:10.1093/nar/gki378 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

John Besemer and Mark Borodovsky: GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
Nucl. Acids Res. 2005 33: W451-W454; doi:10.1093/nar/gki487 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Gary H. Van Domselaar, Paul Stothard, Savita Shrivastava, Joseph A. Cruz, AnChi Guo, Xiaoli Dong, Paul Lu, Duane Szafron, Russ Greiner, and David S. Wishart: BASys: a web server for automated bacterial genome annotation
Nucl. Acids Res. 2005 33: W455-W459; doi:10.1093/nar/gki593 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Fátima Al-Shahrour, Pablo Minguez, Juan M. Vaquerizas, Lucía Conde, and Joaquín Dopazo: BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments
Nucl. Acids Res. 2005 33: W460-W464; doi:10.1093/nar/gki456 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Mario Stanke and Burkhard Morgenstern: AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
Nucl. Acids Res. 2005 33: W465-W467; doi:10.1093/nar/gki458 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Páll Ísólfur Ólason: Integrating protein annotation resources through the Distributed Annotation System
Nucl. Acids Res. 2005 33: W468-W470; doi:10.1093/nar/gki463 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Stéphane Cruveiller, Jérôme Le Saux, David Vallenet, Aurélie Lajus, Stéphanie Bocs, and Claudine Médigue: MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes
Nucl. Acids Res. 2005 33: W471-W479; doi:10.1093/nar/gki498 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Lei Bao, Mi Zhou, and Yan Cui: nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms
Nucl. Acids Res. 2005 33: W480-W482; doi:10.1093/nar/gki372 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Jinho Yoo, Bonghee Seo, and Yangseok Kim: SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis
Nucl. Acids Res. 2005 33: W483-W488; doi:10.1093/nar/gki428 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Ruifang Zhang, Zanhua Zhu, Hongming Zhu, Tu Nguyen, Fengxia Yao, Kun Xia, Desheng Liang, and Chunyu Liu: SNP Cutter: a comprehensive tool for SNP PCR–RFLP assay design
Nucl. Acids Res. 2005 33: W489-W492; doi:10.1093/nar/gki358 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material][Supplementary Material] OPEN ACCESS ARTICLE

David Savage, Jacqueline Batley, Tim Erwin, Erica Logan, Christopher G. Love, Geraldine A. C. Lim, Emmanuel Mongin, Gary Barker, German C. Spangenberg, and David Edwards: SNPServer: a real-time SNP discovery tool
Nucl. Acids Res. 2005 33: W493-W495; doi:10.1093/nar/gki462 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Matthias Klaften and Martin Hrabé de Angelis: ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants
Nucl. Acids Res. 2005 33: W496-W500; doi:10.1093/nar/gki430 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Lucía Conde, Juan M. Vaquerizas, Carles Ferrer-Costa, Xavier de la Cruz, Modesto Orozco, and Joaquín Dopazo: PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes
Nucl. Acids Res. 2005 33: W501-W505; doi:10.1093/nar/gki476 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Eric W. Klee, Kyong Jin Shim, Michael A. Pickart, Stephen C. Ekker, and Lynda B. M. Ellis: AMOD: a morpholino oligonucleotide selection tool
Nucl. Acids Res. 2005 33: W506-W511; doi:10.1093/nar/gki453 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Bernard Fertil, Matthieu Massin, Sylvain Lespinats, Caroline Devic, Philippe Dumee, and Alain Giron: GENSTYLE: exploration and analysis of DNA sequences with genomic signature
Nucl. Acids Res. 2005 33: W512-W515; doi:10.1093/nar/gki489 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Jakob Fredslund, Leif Schauser, Lene H. Madsen, Niels Sandal, and Jens Stougaard: PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs
Nucl. Acids Res. 2005 33: W516-W520; doi:10.1093/nar/gki425 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Roman Rydzanicz, X. Sharon Zhao, and Philip E. Johnson: Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production
Nucl. Acids Res. 2005 33: W521-W525; doi:10.1093/nar/gki380 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Andreas Grote, Karsten Hiller, Maurice Scheer, Richard Münch, Bernd Nörtemann, Dietmar C. Hempel, and Dieter Jahn: JCat: a novel tool to adapt codon usage of a target gene to its potential expression host
Nucl. Acids Res. 2005 33: W526-W531; doi:10.1093/nar/gki376 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Dirk Pöhler, Nadine Werner, Rasmus Steinkamp, and Burkhard Morgenstern: Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC
Nucl. Acids Res. 2005 33: W532-W534; doi:10.1093/nar/gki386 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Per Eystein Sæbø, Sten Morten Andersen, Jon Myrseth, Jon K. Laerdahl, and Torbjørn Rognes: PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology
Nucl. Acids Res. 2005 33: W535-W539; doi:10.1093/nar/gki423 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Laurent Noé and Gregory Kucherov: YASS: enhancing the sensitivity of DNA similarity search
Nucl. Acids Res. 2005 33: W540-W543; doi:10.1093/nar/gki478 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

John Rachlin, Chunming Ding, Charles Cantor, and Simon Kasif: MuPlex: multi-objective multiplex PCR assay design
Nucl. Acids Res. 2005 33: W544-W547; doi:10.1093/nar/gki377 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Steven Ringquist, Christopher Pecoraro, Crystal M. S. Gilchrist, Alexis Styche, William A. Rudert, Panagiotis V. Benos, and Massimo Trucco: SOP³v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms
Nucl. Acids Res. 2005 33: W548-W552; doi:10.1093/nar/gki483 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Chung-Yen Lin, Fan-Kai Lin, Chieh Hua Lin, Li-Wei Lai, Hsiu-Jun Hsu, Shu-Hwa Chen, and Chao A. Hsiung: POWER: PhylOgenetic WEb Repeater—an integrated and user-optimized framework for biomolecular phylogenetic analysis
Nucl. Acids Res. 2005 33: W553-W556; doi:10.1093/nar/gki494 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Stéphane Guindon, Franck Lethiec, Patrice Duroux, and Olivier Gascuel: PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference
Nucl. Acids Res. 2005 33: W557-W559; doi:10.1093/nar/gki352 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Sacha A. F. T. van Hijum, Aldert L. Zomer, Oscar P. Kuipers, and Jan Kok: Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies
Nucl. Acids Res. 2005 33: W560-W566; doi:10.1093/nar/gki356 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Rasmus Wernersson: FeatureExtract—extraction of sequence annotation made easy
Nucl. Acids Res. 2005 33: W567-W569; doi:10.1093/nar/gki388 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Alejandro Panjkovich, Tomás Norambuena, and Francisco Melo: dnaMATE: a consensus melting temperature prediction server for short DNA sequences
Nucl. Acids Res. 2005 33: W570-W572; doi:10.1093/nar/gki379 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Eivind Tøstesen, Geir Ivar Jerstad, and Eivind Hovig: Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles
Nucl. Acids Res. 2005 33: W573-W576; doi:10.1093/nar/gki424 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Nicholas R. Markham and Michael Zuker: DINAMelt web server for nucleic acid melting prediction
Nucl. Acids Res. 2005 33: W577-W581; doi:10.1093/nar/gki591 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Zeynep Arziman, Thomas Horn, and Michael Boutros: E-RNAi: a web application to design optimized RNAi constructs
Nucl. Acids Res. 2005 33: W582-W588; doi:10.1093/nar/gki468 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Yuki Naito, Tomoyuki Yamada, Takahiro Matsumiya, Kumiko Ui-Tei, Kaoru Saigo, and Shinichi Morishita: dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference
Nucl. Acids Res. 2005 33: W589-W591; doi:10.1093/nar/gki419 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

André Boorsma, Barrett C. Foat, Daniel Vis, Frans Klis, and Harmen J. Bussemaker: T-profiler: scoring the activity of predefined groups of genes using gene expression data
Nucl. Acids Res. 2005 33: W592-W595; doi:10.1093/nar/gki484 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Chang-Jiun Wu and Simon Kasif: GEMS: a web server for biclustering analysis of expression data
Nucl. Acids Res. 2005 33: W596-W599; doi:10.1093/nar/gki469 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

P. Clote: RNALOSS: a web server for RNA locally optimal secondary structures
Nucl. Acids Res. 2005 33: W600-W604; doi:10.1093/nar/gki382 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

A. Xayaphoummine, T. Bucher, and H. Isambert: Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots
Nucl. Acids Res. 2005 33: W605-W610; doi:10.1093/nar/gki447 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Rasmus Wernersson and Henrik Bjørn Nielsen: OligoWiz 2.0—integrating sequence feature annotation into the design of microarray probes
Nucl. Acids Res. 2005 33: W611-W615; doi:10.1093/nar/gki399 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Juan M. Vaquerizas, Lucía Conde, Patricio Yankilevich, Amaya Cabezón, Pablo Minguez, Ramón Díaz-Uriarte, Fátima Al-Shahrour, Javier Herrero, and Joaquín Dopazo: GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
Nucl. Acids Res. 2005 33: W616-W620; doi:10.1093/nar/gki500 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Hee-Joon Chung, Chan Hee Park, Mi Ryung Han, Seokho Lee, Jung Hun Ohn, Jihoon Kim, Jihun Kim, and Ju Han Kim: ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics
Nucl. Acids Res. 2005 33: W621-W626; doi:10.1093/nar/gki450 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Albert Hsiao, Trey Ideker, Jerrold M. Olefsky, and Shankar Subramaniam: VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data
Nucl. Acids Res. 2005 33: W627-W632; doi:10.1093/nar/gki443 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Bernhard Mlecnik, Marcel Scheideler, Hubert Hackl, Jürgen Hartler, Fatima Sanchez-Cabo, and Zlatko Trajanoski: PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways
Nucl. Acids Res. 2005 33: W633-W637; doi:10.1093/nar/gki391 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Michael Psarros, Steffen Heber, Manuela Sick, Gnanasekaran Thoppae, Keith Harshman, and Beate Sick: RACE: Remote Analysis Computation for gene Expression data
Nucl. Acids Res. 2005 33: W638-W643; doi:10.1093/nar/gki490 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Chiara Romualdi, Nicola Vitulo, Micky Del Favero, and Gerolamo Lanfranchi: MIDAW: a web tool for statistical analysis of microarray data
Nucl. Acids Res. 2005 33: W644-W649; doi:10.1093/nar/gki497 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Jakob H. Havgaard, Rune B. Lyngsø, and Jan Gorodkin: The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
Nucl. Acids Res. 2005 33: W650-W653; doi:10.1093/nar/gki473 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Shobhit Gupta, Martin Vingron, and Stefan A. Haas: T-STAG: resource and web-interface for tissue-specific transcripts and genes
Nucl. Acids Res. 2005 33: W654-W658; doi:10.1093/nar/gki350 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Sachiyo Aburatani, Kousuke Goto, Shigeru Saito, Hiroyuki Toh, and Katsuhisa Horimoto: ASIAN: a web server for inferring a regulatory network framework from gene expression profiles
Nucl. Acids Res. 2005 33: W659-W664; doi:10.1093/nar/gki446 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Giovanni Lavorgna, Riccardo Triunfo, Federico Santoni, Ugo Orfanelli, Sara Noci, Alessandro Bulfone, Gianluigi Zanetti, and Giorgio Casari: AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts
Nucl. Acids Res. 2005 33: W665-W668; doi:10.1093/nar/gki448 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang: TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences
Nucl. Acids Res. 2005 33: W669-W672; doi:10.1093/nar/gki436 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Xin Wu, Michael G. Walker, Jingchu Luo, and Liping Wei: GBA server: EST-based digital gene expression profiling
Nucl. Acids Res. 2005 33: W673-W676; doi:10.1093/nar/gki480 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang: OrfPredictor: predicting protein-coding regions in EST-derived sequences
Nucl. Acids Res. 2005 33: W677-W680; doi:10.1093/nar/gki394 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Namshin Kim, Dajeong Lim, Sanghyuk Lee, and Heebal Kim: ASePCR: alternative splicing electronic RT–PCR in multiple tissues and organs
Nucl. Acids Res. 2005 33: W681-W685; doi:10.1093/nar/gki407 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Peter Schattner, Angela N. Brooks, and Todd M. Lowe: The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
Nucl. Acids Res. 2005 33: W686-W689; doi:10.1093/nar/gki366 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Cei Abreu-Goodger and Enrique Merino: RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements
Nucl. Acids Res. 2005 33: W690-W692; doi:10.1093/nar/gki445 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Jean Pylouster, Catherine Sénamaud-Beaufort, and Tula Ester Saison-Behmoaras: WEBSAGE: a web tool for visual analysis of differentially expressed human SAGE tags
Nucl. Acids Res. 2005 33: W693-W695; doi:10.1093/nar/gki444 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Ventsislav Rusinov, Vesselin Baev, Ivan Nikiforov Minkov, and Martin Tabler: MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence
Nucl. Acids Res. 2005 33: W696-W700; doi:10.1093/nar/gki364 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Yuanji Zhang: miRU: an automated plant miRNA target prediction server
Nucl. Acids Res. 2005 33: W701-W704; doi:10.1093/nar/gki383 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Andreas Bohne-Lang, Wolf-Dieter Groch, and René Ranzinger: AISMIG—an interactive server-side molecule image generator
Nucl. Acids Res. 2005 33: W705-W709; doi:10.1093/nar/gki438 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

A. Goesmann, B. Linke, D. Bartels, M. Dondrup, L. Krause, H. Neuweger, S. Oehm, T. Paczian, A. Wilke, and F. Meyer: BRIGEP—the BRIDGE-based genome–transcriptome–proteome browser
Nucl. Acids Res. 2005 33: W710-W716; doi:10.1093/nar/gki400 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Marco Masseroli, Osvaldo Galati, and Francesco Pinciroli: GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists
Nucl. Acids Res. 2005 33: W717-W723; doi:10.1093/nar/gki454 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Stephen Rudd and Igor V. Tetko: Éclair—a web service for unravelling species origin of sequences sampled from mixed host interfaces
Nucl. Acids Res. 2005 33: W724-W727; doi:10.1093/nar/gki434 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

David M. Aanensen and Brian G. Spratt: The multilocus sequence typing network: mlst.net
Nucl. Acids Res. 2005 33: W728-W733; doi:10.1093/nar/gki415 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Tsute Chen, Kevin Abbey, Wen-jie Deng, and Meng-chuan Cheng: The bioinformatics resource for oral pathogens
Nucl. Acids Res. 2005 33: W734-W740; doi:10.1093/nar/gki361 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Bing Zhang, Stefan Kirov, and Jay Snoddy: WebGestalt: an integrated system for exploring gene sets in various biological contexts
Nucl. Acids Res. 2005 33: W741-W748; doi:10.1093/nar/gki475 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Peter Juvan, Janez Demsar, Gad Shaulsky, and Blaz Zupan: GenePath: from mutations to genetic networks and back
Nucl. Acids Res. 2005 33: W749-W752; doi:10.1093/nar/gki426 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Material] OPEN ACCESS ARTICLE

Taro L. Saito, Jun Sese, Yoichiro Nakatani, Fumi Sano, Masashi Yukawa, Yoshikazu Ohya, and Shinichi Morishita: Data mining tools for the Saccharomyces cerevisiae morphological database
Nucl. Acids Res. 2005 33: W753-W757; doi:10.1093/nar/gki451 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

M. A. van Driel, K. Cuelenaere, P. P. C. W. Kemmeren, J. A. M. Leunissen, H. G. Brunner, and Gert Vriend: GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases
Nucl. Acids Res. 2005 33: W758-W761; doi:10.1093/nar/gki435 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Purvesh Khatri, Sivakumar Sellamuthu, Pooja Malhotra, Kashyap Amin, Arina Done, and Sorin Draghici: Recent additions and improvements to the Onto-Tools
Nucl. Acids Res. 2005 33: W762-W765; doi:10.1093/nar/gki472 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

M. L. Hekkelman and G. Vriend: MRS: a fast and compact retrieval system for biological data
Nucl. Acids Res. 2005 33: W766-W769; doi:10.1093/nar/gki422 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Benjamin R. Landsteiner, Michael R. Olson, and Robert Rutherford: Current Comparative Table (CCT) automates customized searches of dynamic biological databases
Nucl. Acids Res. 2005 33: W770-W773; doi:10.1093/nar/gki432 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Thomas Goetz and Claus-Wilhelm von der Lieth: PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts
Nucl. Acids Res. 2005 33: W774-W778; doi:10.1093/nar/gki429 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Holger Maier, Stefanie Döhr, Korbinian Grote, Sean O'Keeffe, Thomas Werner, Martin Hrabé de Angelis, and Ralf Schneider: LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts
Nucl. Acids Res. 2005 33: W779-W782; doi:10.1093/nar/gki417 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

Andreas Doms and Michael Schroeder: GoPubMed: exploring PubMed with the Gene Ontology
Nucl. Acids Res. 2005 33: W783-W786; doi:10.1093/nar/gki470 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] OPEN ACCESS ARTICLE

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