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Secondary structure

Super-secondary structure

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    Software in Molecular Biology (2005):

    An overview about molecular biological software is given each year in a special issue of Nucleic Acids Research. The published articles are very useful to get fast and qualified answers to related questions. Please enjoy the list of articles and web resources published in July 2005:

  • 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. 33: W3-W24

  • 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. 33: W25-W28

  • 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. 33: W29-W35

  • 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. 33: W36-W38

  • 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. 33: W39-W43

  • 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. 33: W44-W49

  • 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. 33: W50-W55

  • Gabriela G. Loots and Ivan Ovcharenko anthology of comparative genomic tools
    Nucl. Acids Res. 33: W56-W64

  • Jérôme Gracy and Laurent Chiche
    PAT: a protein analysis toolkit for integrated biocomputing on the web
    Nucl. Acids Res. 33: W65-W71

  • J. Cheng, A. Z. Randall, M. J. Sweredoski, and P. Baldi
    SCRATCH: a protein structure and structural feature prediction server
    Nucl. Acids Res. 33: W72-W76

  • Ling-Hong Hung, Shing-Chung Ngan, Tianyun Liu, and Ram Samudrala
    PROTINFO: new algorithms for enhanced protein structure predictions
    Nucl. Acids Res. 33: W77-W80

  • Ori Sasson and Michal Linial
    ProTarget: automatic prediction of protein structure novelty
    Nucl. Acids Res. 33: W81-W84

  • 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. 33: W85-W88

  • Roman A. Laskowski, James D. Watson, and Janet M. Thornton
    ProFunc: a server for predicting protein function from 3D structure
    Nucl. Acids Res. 33: W89-W93

  • Guoli Wang and Roland L. Dunbrack, Jr
    PISCES: recent improvements to a PDB sequence culling server
    Nucl. Acids Res. 33: W94-W98

  • 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. 33: W99-W104

  • 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. 33: W105-W110

  • 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. 33: W111-W115

  • E. Quevillon, V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, and R. Lopez
    InterProScan: protein domains identifier
    Nucl. Acids Res. 33: W116-W120

  • 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. 33: W121-W125

  • 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. 33: W126-W129

  • Ganesan Pugalenthi, Govindaraju Archunan, and Ramanathan Sowdhamini
    DIAL: a web-based server for the automatic identification of structural domains in proteins
    Nucl. Acids Res. 33: W130-W132

  • 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. 33: W133-W137

  • 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. 33: W138-W142

  • 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. 33: W143-W147

  • 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. 33: W148-W153

  • Manish Kumar, Manoj Bhasin, Navjot K. Natt, and G. P. S. Raghava
    BhairPred: prediction of Β-hairpins in a protein from multiple alignment information using ANN and SVM techniques
    Nucl. Acids Res. 33: W154-W159

  • Richard A. George, Kuang Lin, and Jaap Heringa
    Scooby-domain: prediction of globular domains in protein sequence
    Nucl. Acids Res. 33: W160-W163

  • M. Michael Gromiha, Shandar Ahmad, and Makiko Suwa
    TMBETA-NET: discrimination and prediction of membrane spanning Β-strands in outer membrane proteins
    Nucl. Acids Res. 33: W164-W167

  • Urmila Kulkarni-Kale, Shriram Bhosle, and A. S. Kolaskar
    CEP: a conformational epitope prediction server
    Nucl. Acids Res. 33: W168-W171

  • 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. 33: W172-W179

  • Guang Lan Zhang, Kellathur N. Srinivasan, Anitha Veeramani, J. Thomas August, and Vladimir Brusic
    PREDBALB/c: a system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse
    Nucl. Acids Res. 33: W180-W183

  • 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. 33: W184-W187

  • Andrew G. Garrow, Alison Agnew, and David R. Westhead
    TMB-Hunt: a web server to screen sequence sets for transmembrane Β-barrel proteins
    Nucl. Acids Res. 33: W188-W192

  • 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. 33: W193-W197

  • 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. 33: W198-W201

  • 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. 33: W202-W207

  • 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. 33: W208-W213

  • Andreas Bohne-Lang and Claus-Wilhelm von der Lieth
    GlyProt: in silico glycosylation of proteins
    Nucl. Acids Res. 33: W214-W219

  • Pankaj Kamra, Rajesh S. Gokhale, and Debasisa Mohanty
    SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites
    Nucl. Acids Res. 33: W220-W225

  • 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. 33: W226-W229

  • F. Ferrè and P. Clote
    DiANNA: a web server for disulfide connectivity prediction
    Nucl. Acids Res. 33: W230-W232

  • 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. 33: W233-W238

  • Markus Gruber, Johannes Söding, and Andrei N. Lupas
    REPPER—repeats and their periodicities in fibrous proteins
    Nucl. Acids Res. 33: W239-W243

  • Johannes Söding, Andreas Biegert, and Andrei N. Lupas
    The HHpred interactive server for protein homology detection and structure prediction
    Nucl. Acids Res. 33: W244-W248

  • Iddo Friedberg and Adam Godzik
    Fragnostic: walking through protein structure space
    Nucl. Acids Res. 33: W249-W251

  • 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. 33: W252-W254

  • 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. 33: W255-W261

  • 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. 33: W262-W266

  • David La and Dennis R. Livesay
    MINER: software for phylogenetic motif identification
    Nucl. Acids Res. 33: W267-W270

  • S. Roepcke, P. Fiziev, P. H. Seeburg, and M. Vingron
    SVC: structured visualization of evolutionary sequence conservation
    Nucl. Acids Res. 33: W271-W273

  • 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. 33: W274-W276

  • Iris Bahir and Michal Linial
    ProTeus: identifying signatures in protein termini
    Nucl. Acids Res. 33: W277-W280

  • 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. 33: W281-W283

  • Lukasz Jaroszewski, Leszek Rychlewski, Zhanwen Li, Weizhong Li, and Adam Godzik
    FFAS03: a server for profile–profile sequence alignments
    Nucl. Acids Res. 33: W284-W288

  • V. A. Simossis and J. Heringa
    PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
    Nucl. Acids Res. 33: W289-W294

  • 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. 33: W295-W298

  • 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. 33: W299-W302

  • 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. 33: W303-W305

  • Emidio Capriotti, Piero Fariselli, and Rita Casadio
    I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
    Nucl. Acids Res. 33: W306-W310

  • Jessica Dantzer, Charles Moad, Randy Heiland, and Sean Mooney
    MutDB services: interactive structural analysis of mutation data
    Nucl. Acids Res. 33: W311-W314

  • William C. Ray
    MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features
    Nucl. Acids Res. 33: W315-W319

  • Cédric Binisti, Ahmed Ali Salim, and Pierre Tufféry
    PPG: online generation of protein pictures and animations
    Nucl. Acids Res. 33: W320-W323

  • 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. 33: W324-W325

  • Didier Croes, Fabian Couche, Shoshana J. Wodak, and Jacques van Helden
    Metabolic PathFinding: inferring relevant pathways in biochemical networks
    Nucl. Acids Res. 33: W326-W330

  • Utkan Ogmen, Ozlem Keskin, A. Selim Aytuna, Ruth Nussinov, and Attila Gursoy
    PRISM: protein interactions by structural matching
    Nucl. Acids Res. 33: W331-W336

  • Alexandra Shulman-Peleg, Ruth Nussinov, and Haim J. Wolfson
    SiteEngines: recognition and comparison of binding sites and protein–protein interfaces
    Nucl. Acids Res. 33: W337-W341

  • Jens Kleinjung and Franca Fraternali
    POPSCOMP: an automated interaction analysis of biomolecular complexes
    Nucl. Acids Res. 33: W342-W346

  • Osvaldo Graña, Volker A. Eyrich, Florencio Pazos, Burkhard Rost, and Alfonso Valencia
    EVAcon: a protein contact prediction evaluation service
    Nucl. Acids Res. 33: W347-W351

  • 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. 33: W352-W357

  • 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. 33: W358-W362

  • Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, and Haim J. Wolfson
    PatchDock and SymmDock: servers for rigid and symmetric docking
    Nucl. Acids Res. 33: W363-W367

  • John C. Gordon, Jonathan B. Myers, Timothy Folta, Valia Shoja, Lenwood S. Heath, and Alexey Onufriev
    H++: a server for estimating pKas and adding missing hydrogens to macromolecules
    Nucl. Acids Res. 33: W368-W371

  • Maria A. Miteva, Pierre Tufféry, and Bruno O. Villoutreix
    PCE: web tools to compute protein continuum electrostatics
    Nucl. Acids Res. 33: W372-W375

  • 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. 33: W376-W381

  • Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, and Luis Serrano
    The FoldX web server: an online force field
    Nucl. Acids Res. 33: W382-W388

  • 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. 33: W389-W392

  • 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. 33: W393-W396

  • 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. 33: W397-W402

  • Ivan Ovcharenko and Marcelo A. Nobrega
    Identifying synonymous regulatory elements in vertebrate genomes
    Nucl. Acids Res. 33: W403-W407

  • 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. 33: W408-W411

  • Guandong Wang, Taotao Yu, and Weixiong Zhang
    WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar
    Nucl. Acids Res. 33: W412-W416

  • 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. 33: W417-W422

  • 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. 33: W423-W426

  • Matti Kankainen and Liisa Holm
    POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets
    Nucl. Acids Res. 33: W427-W431

  • 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. 33: W432-W437

  • 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. 33: W438-W441

  • 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. 33: W442-W446

  • Eugene Berezikov, Victor Guryev, and Edwin Cuppen
    CONREAL web server: identification and visualization of conserved transcription factor binding sites
    Nucl. Acids Res. 33: W447-W450

  • John Besemer and Mark Borodovsky
    GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
    Nucl. Acids Res. 33: W451-W454

  • 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. 33: W455-W459

  • 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. 33: W460-W464

  • Mario Stanke and Burkhard Morgenstern
    AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
    Nucl. Acids Res. 33: W465-W467

  • Páll Ísólfur Ólason
    Integrating protein annotation resources through the Distributed Annotation System
    Nucl. Acids Res. 33: W468-W470

  • 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. 33: W471-W479

  • Lei Bao, Mi Zhou, and Yan Cui
    nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms
    Nucl. Acids Res. 33: W480-W482

  • Jinho Yoo, Bonghee Seo, and Yangseok Kim
    SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis
    Nucl. Acids Res. 33: W483-W488

  • 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. 33: W489-W492

  • 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. 33: W493-W495

  • 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. 33: W496-W500

  • 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. 33: W501-W505

  • 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. 33: W506-W511

  • 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. 33: W512-W515

  • 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. 33: W516-W520

  • 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. 33: W521-W525

  • 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. 33: W526-W531

  • Dirk Pöhler, Nadine Werner, Rasmus Steinkamp, and Burkhard Morgenstern
    Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC
    Nucl. Acids Res. 33: W532-W534

  • Per Eystein Sœbø, 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. 33: W535-W539

  • Laurent Noé and Gregory Kucherov
    YASS: enhancing the sensitivity of DNA similarity search
    Nucl. Acids Res. 33: W540-W543

  • John Rachlin, Chunming Ding, Charles Cantor, and Simon Kasif
    MuPlex: multi-objective multiplex PCR assay design
    Nucl. Acids Res. 33: W544-W547

  • 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. 33: W548-W552

  • 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. 33: W553-W556

  • Stéphane Guindon, Franck Lethiec, Patrice Duroux, and Olivier Gascuel
    PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference
    Nucl. Acids Res. 33: W557-W559

  • 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. 33: W560-W566

  • Rasmus Wernersson
    FeatureExtract—extraction of sequence annotation made easy
    Nucl. Acids Res. 33: W567-W569

  • Alejandro Panjkovich, Tomás Norambuena, and Francisco Melo
    dnaMATE: a consensus melting temperature prediction server for short DNA sequences
    Nucl. Acids Res. 33: W570-W572

  • Eivind Tøstesen, Geir Ivar Jerstad, and Eivind Hovig analysis of partly melted DNA conformations using stitch profiles
    Nucl. Acids Res. 33: W573-W576

  • Nicholas R. Markham and Michael Zuker
    DINAMelt web server for nucleic acid melting prediction
    Nucl. Acids Res. 33: W577-W581

  • Zeynep Arziman, Thomas Horn, and Michael Boutros
    E-RNAi: a web application to design optimized RNAi constructs
    Nucl. Acids Res. 33: W582-W588

  • 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. 33: W589-W591

  • 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. 33: W592-W595

  • Chang-Jiun Wu and Simon Kasif
    GEMS: a web server for biclustering analysis of expression data
    Nucl. Acids Res. 33: W596-W599

  • P. Clote
    RNALOSS: a web server for RNA locally optimal secondary structures
    Nucl. Acids Res. 33: W600-W604

  • 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. 33: W605-W610

  • Rasmus Wernersson and Henrik Bjørn Nielsen
    OligoWiz 2.0—integrating sequence feature annotation into the design of microarray probes
    Nucl. Acids Res. 33: W611-W615

  • 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. 33: W616-W620

  • 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. 33: W621-W626

  • 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. 33: W627-W632

  • 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. 33: W633-W637

  • Michael Psarros, Steffen Heber, Manuela Sick, Gnanasekaran Thoppae, Keith Harshman, and Beate Sick
    RACE: Remote Analysis Computation for gene Expression data
    Nucl. Acids Res. 33: W638-W643

  • Chiara Romualdi, Nicola Vitulo, Micky Del Favero, and Gerolamo Lanfranchi
    MIDAW: a web tool for statistical analysis of microarray data
    Nucl. Acids Res. 33: W644-W649

  • 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. 33: W650-W653

  • Shobhit Gupta, Martin Vingron, and Stefan A. Haas
    T-STAG: resource and web-interface for tissue-specific transcripts and genes
    Nucl. Acids Res. 33: W654-W658

  • 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. 33: W659-W664

  • 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. 33: W665-W668

  • Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang
    TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences
    Nucl. Acids Res. 33: W669-W672

  • Xin Wu, Michael G. Walker, Jingchu Luo, and Liping Wei
    GBA server: EST-based digital gene expression profiling
    Nucl. Acids Res. 33: W673-W676

  • Xiang Jia Min, Gregory Butler, Reginald Storms, and Adrian Tsang
    OrfPredictor: predicting protein-coding regions in EST-derived sequences
    Nucl. Acids Res. 33: W677-W680

  • Namshin Kim, Dajeong Lim, Sanghyuk Lee, and Heebal Kim
    ASePCR: alternative splicing electronic RT–PCR in multiple tissues and organs
    Nucl. Acids Res. 33: W681-W685

  • 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. 33: W686-W689

  • Cei Abreu-Goodger and Enrique Merino
    RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements
    Nucl. Acids Res. 33: W690-W692

  • 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. 33: W693-W695

  • 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. 33: W696-W700

  • Yuanji Zhang
    miRU: an automated plant miRNA target prediction server
    Nucl. Acids Res. 33: W701-W704

  • Andreas Bohne-Lang, Wolf-Dieter Groch, and René Ranzinger
    AISMIG—an interactive server-side molecule image generator
    Nucl. Acids Res. 33: W705-W709

  • 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. 33: W710-W716

  • 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. 33: W717-W723

  • Stephen Rudd and Igor V. Tetko
    Éclair—a web service for unravelling species origin of sequences sampled from mixed host interfaces
    Nucl. Acids Res. 33: W724-W727

  • David M. Aanensen and Brian G. Spratt
    The multilocus sequence typing network:
    Nucl. Acids Res. 33: W728-W733

  • Tsute Chen, Kevin Abbey, Wen-jie Deng, and Meng-chuan Cheng
    The bioinformatics resource for oral pathogens
    Nucl. Acids Res. 33: W734-W740

  • Bing Zhang, Stefan Kirov, and Jay Snoddy
    WebGestalt: an integrated system for exploring gene sets in various biological contexts
    Nucl. Acids Res. 33: W741-W748

  • Peter Juvan, Janez Demsar, Gad Shaulsky, and Blaz Zupan
    GenePath: from mutations to genetic networks and back
    Nucl. Acids Res. 33: W749-W752

  • 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. 33: W753-W757

  • 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. 33: W758-W761

  • Purvesh Khatri, Sivakumar Sellamuthu, Pooja Malhotra, Kashyap Amin, Arina Done, and Sorin Draghici
    Recent additions and improvements to the Onto-Tools
    Nucl. Acids Res. 33: W762-W765

  • M. L. Hekkelman and G. Vriend
    MRS: a fast and compact retrieval system for biological data
    Nucl. Acids Res. 33: W766-W769

  • Benjamin R. Landsteiner, Michael R. Olson, and Robert Rutherford
    Current Comparative Table (CCT) automates customized searches of dynamic biological databases
    Nucl. Acids Res. 33: W770-W773

  • Thomas Goetz and Claus-Wilhelm von der Lieth
    PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts
    Nucl. Acids Res. 33: W774-W778

  • 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. 33: W779-W782

  • Andreas Doms and Michael Schroeder
    GoPubMed: exploring PubMed with the Gene Ontology
    Nucl. Acids Res. 33: W783-W786


Latest update: August 4, 2005

Ralf Koebnik
Institut für Genetik
Abt. Pflanzengenetik
Weinbergweg 10
06120 Halle/Saale
Telefon: 0345 / 55 26 293 (Büro) bzw. 296 (Labor)
Fax: 0345 / 55 27 151
Email: koebnik (at)
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