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
  Dcode.org 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 structureÐactivity 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 GPCRÐG-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
  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. 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 profileÐprofile 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 proteinÐprotein 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 pK_as 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 PCRÐRFLP 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
  Stitchprofiles.uio.no: 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: mlst.net
  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) gmx.de
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