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Sequence comparisons

Homology searches

Motif searches

Hidden Markov models

Hydrophobicity analyses

Topology and helix packing

Protein localization

Secondary structure

Super-secondary structure

3D structure


    Software in Molecular Biology (2003):

    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 published in July 2003:

  • Krzysztof Ginalski and Leszek Rychlewski
    Detection of reliable and unexpected protein fold predictions using 3D-Jury
    Nucl. Acids Res. 31: 3291-3292.

  • Phil Carter, Claus A. F. Andersen, and Burkhard Rost
    DSSPcont: continuous secondary structure assignments for proteins
    Nucl. Acids Res. 31: 3293-3295.

  • Ling-Hong Hung and Ram Samudrala
    PROTINFO: secondary and tertiary protein structure prediction
    Nucl. Acids Res. 31: 3296-3299.

  • Burkhard Rost and Jinfeng Liu
    The PredictProtein server
    Nucl. Acids Res. 31: 3300-3304.

  • Michal A. Kurowski and Janusz M. Bujnicki
    GeneSilico protein structure prediction meta-server
    Nucl. Acids Res. 31: 3305-3307.

  • Volker A. Eyrich and Burkhard Rost
    META-PP: single interface to crucial prediction servers
    Nucl. Acids Res. 31: 3308-3310.

  • Ingrid Y. Y. Koh, Volker A. Eyrich, Marc A. Marti-Renom, Dariusz Przybylski, Mallur S. Madhusudhan, Narayanan Eswar, Osvaldo Graña, Florencio Pazos, Alfonso Valencia, Andrej Sali, and Burkhard Rost
    EVA: evaluation of protein structure prediction servers
    Nucl. Acids Res. 31: 3311-3315.

  • Leigh Willard, Anuj Ranjan, Haiyan Zhang, Hassan Monzavi, Robert F. Boyko, Brian D. Sykes, and David S. Wishart
    VADAR: a web server for quantitative evaluation of protein structure quality
    Nucl. Acids Res. 31: 3316-3319.

  • Patrice Gouet, Xavier Robert, and Emmanuel Courcelle
    ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins
    Nucl. Acids Res. 31: 3320-3323.

  • Mike P. Liang, D. Rey Banatao, Teri E. Klein, Douglas L. Brutlag, and Russ B. Altman
    WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures
    Nucl. Acids Res. 31: 3324-3327.

  • Steven P. Bennett, Lin Lu, and Douglas L. Brutlag
    3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs
    Nucl. Acids Res. 31: 3328-3332.

  • Anna Gaulton and Teresa K. Attwood
    Motif3D: relating protein sequence motifs to 3D structure
    Nucl. Acids Res. 31: 3333-3336.

  • Rajesh Nair and Burkhard Rost
    LOC3D: annotate sub-cellular localization for protein structures
    Nucl. Acids Res. 31: 3337-3340.

  • Alexander Stark and Robert B. Russell
    Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
    Nucl. Acids Res. 31: 3341-3344.

  • M. Madan Babu
    NCI: a server to identify non-canonical interactions in protein structures
    Nucl. Acids Res. 31: 3345-3348.

  • Razif R. Gabdoulline, Rebecca C. Wade, and Dirk Walther
    MolSurfer: a macromolecular interface navigator
    Nucl. Acids Res. 31: 3349-3351.

  • T. Andrew Binkowski, Shapor Naghibzadeh, and Jie Liang
    CASTp: Computed Atlas of Surface Topography of proteins
    Nucl. Acids Res. 31: 3352-3355.

  • A. S. Z. Hussain, Ch. Kiran Kumar, C. K. Rajesh, S. S. Sheik, and K. Sekar
    SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules
    Nucl. Acids Res. 31: 3356-3358.

  • Zsuzsanna Dosztányi, Csaba Magyar, Gábor E. Tusnády, Miklós Cserzo, András Fiser, and István Simon
    Servers for sequence–structure relationship analysis and prediction
    Nucl. Acids Res. 31: 3359-3363.

  • Luigi Cavallo, Jens Kleinjung, and Franca Fraternali
    POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level
    Nucl. Acids Res. 31: 3364-3366.

  • Takeshi Kawabata
    MATRAS: a program for protein 3D structure comparison
    Nucl. Acids Res. 31: 3367-3369.

  • Adam Zemla
    LGA: a method for finding 3D similarities in protein structures
    Nucl. Acids Res. 31: 3370-3374.

  • Narayanan Eswar, Bino John, Nebojsa Mirkovic, Andras Fiser, Valentin A. Ilyin, Ursula Pieper, Ashley C. Stuart, Marc A. Marti-Renom, M. S. Madhusudhan, Bozidar Yerkovich, and Andrej Sali
    Tools for comparative protein structure modeling and analysis
    Nucl. Acids Res. 31: 3375-3380.

  • Torsten Schwede, Jürgen Kopp, Nicolas Guex, and Manuel C. Peitsch
    SWISS-MODEL: an automated protein homology-modeling server
    Nucl. Acids Res. 31: 3381-3385.

  • Goran Neshich, Roberto C. Togawa, Adauto L. Mancini, Paula R. Kuser, Michel E. B. Yamagishi, Georgios Pappas, Jr, Wellington V. Torres, Tharsis Fonseca e Campos, Leonardo L. Ferreira, Fabio M. Luna, Adilton G. Oliveira, Ronald T. Miura, Marcus K. Inoue, Luiz G. Horita, Dimas F. de Souza, Fabiana Dominiquini, Alexandre Álvaro, Cleber S. Lima, Fabio O. Ogawa, Gabriel B. Gomes, Juliana F. Palandrani, Gabriela F. dos Santos, Esther M. de Freitas, Amanda R. Mattiuz, Ivan C. Costa, Celso L. de Almeida, Savio Souza, Christian Baudet, and Roberto H. Higa
    STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence
    Nucl. Acids Res. 31: 3386-3392.

  • Guy Perrière, Christophe Combet, Simon Penel, Christophe Blanchet, Jean Thioulouse, Christophe Geourjon, Julien Grassot, Céline Charavay, Manolo Gouy, Laurent Duret, and Gilbert Deléage
    Integrated databanks access and sequence/structure analysis services at the PBIL
    Nucl. Acids Res. 31: 3393-3399.

  • Emmanuel Bettler, Roland Krause, Florence Horn, and Gert Vriend
    NRSAS: Nuclear Receptor Structure Analysis Servers
    Nucl. Acids Res. 31: 3400-3403.

  • V. Shanthi, P. Selvarani, Ch. Kiran Kumar, C. S. Mohire, and K. Sekar
    SSEP: secondary structural elements of proteins
    Nucl. Acids Res. 31: 3404-3405.

  • Michael Zuker
    Mfold web server for nucleic acid folding and hybridization prediction
    Nucl. Acids Res. 31: 3406-3415.

  • Mirela Andronescu, Rosalía Aguirre-Hernández, Anne Condon, and Holger H. Hoos
    RNAsoft: a suite of RNA secondary structure prediction and design software tools
    Nucl. Acids Res. 31: 3416-3422.

  • Bjarne Knudsen and Jotun Hein
    Pfold: RNA secondary structure prediction using stochastic context-free grammars
    Nucl. Acids Res. 31: 3423-3428.

  • Ivo L. Hofacker
    Vienna RNA secondary structure server
    Nucl. Acids Res. 31: 3429-3431.

  • Kyungsook Han and Yanga Byun
    PSEUDOVIEWER2: visualization of RNA pseudoknots of any type
    Nucl. Acids Res. 31: 3432-3440.

  • Peter Bengert and Thomas Dandekar
    A software tool-box for analysis of regulatory RNA elements
    Nucl. Acids Res. 31: 3441-3445.

  • Yuh-Jyh Hu
    GPRM: a genetic programming approach to finding common RNA secondary structure elements
    Nucl. Acids Res. 31: 3446-3449.

  • Huanwang Yang, Fabrice Jossinet, Neocles Leontis, Li Chen, John Westbrook, Helen Berman, and Eric Westhof
    Tools for the automatic identification and classification of RNA base pairs
    Nucl. Acids Res. 31: 3450-3460.

  • Javier Herrero, Fátima Al-Shahrour, Ramón Díaz-Uriarte, Álvaro Mateos, Juan M. Vaquerizas, Javier Santoyo, and Joaquín Dopazo
    GEPAS: a web-based resource for microarray gene expression data analysis
    Nucl. Acids Res. 31: 3461-3467.

  • Bert Coessens, Gert Thijs, Stein Aerts, Kathleen Marchal, Frank De Smet, Kristof Engelen, Patrick Glenisson, Yves Moreau, Janick Mathys, and Bart De Moor
    INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis
    Nucl. Acids Res. 31: 3468-3470.

  • Steen Knudsen, Christopher Workman, Thomas Sicheritz-Ponten, and Carsten Friis
    GenePublisher: automated analysis of DNA microarray data
    Nucl. Acids Res. 31: 3471-3476.

  • Nicholas M. Luscombe, Thomas E. Royce, Paul Bertone, Nathaniel Echols, Christine E. Horak, Joseph T. Chang, Michael Snyder, and Mark Gerstein
    ExpressYourself: a modular platform for processing and visualizing microarray data
    Nucl. Acids Res. 31: 3477-3482.

  • Sheng Zhong, Cheng Li, and Wing Hung Wong
    ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis
    Nucl. Acids Res. 31: 3483-3486.

  • Crispin Roven and Harmen J. Bussemaker
    REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
    Nucl. Acids Res. 31: 3487-3490.

  • Henrik Bjørn Nielsen, Rasmus Wernersson, and Steen Knudsen
    Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
    Nucl. Acids Res. 31: 3491-3496.

  • Ramu Chenna, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, and Julie D. Thompson
    Multiple sequence alignment with the Clustal series of programs
    Nucl. Acids Res. 31: 3497-3500.

  • Davinder K. Kohli and Anand K. Bachhawat
    CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics
    Nucl. Acids Res. 31: 3501-3502.

  • Olivier Poirot, Eamonn O'Toole, and Cedric Notredame
    Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments
    Nucl. Acids Res. 31: 3503-3506.

  • Simon Cawley, Lior Pachter, and Marina Alexandersson
    SLAM web server for comparative gene finding and alignment
    Nucl. Acids Res. 31: 3507-3509.

  • Yvonne J. K. Edwards, Tim J. Carver, Tanya Vavouri, Martin Frith, Martin J. Bishop, and Greg Elgar
    Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence
    Nucl. Acids Res. 31: 3510-3517.

  • Scott Schwartz, Laura Elnitski, Mei Li, Matt Weirauch, Cathy Riemer, Arian Smit, NISC Comparative Sequencing Program, Eric D. Green, Ross C. Hardison, and Webb Miller
    MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences
    Nucl. Acids Res. 31: 3518-3524.

  • Nicolas Bray and Lior Pachter
    MAVID multiple alignment server
    Nucl. Acids Res. 31: 3525-3526.

  • Liliana Florea, Michael McClelland, Cathy Riemer, Scott Schwartz, and Webb Miller
    EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae
    Nucl. Acids Res. 31: 3527-3532.

  • Bernett T. K. Lee, Tin Wee Tan, and Shoba Ranganathan
    MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences
    Nucl. Acids Res. 31: 3533-3536.

  • Rasmus Wernersson and Anders Gorm Pedersen
    RevTrans: multiple alignment of coding DNA from aligned amino acid sequences
    Nucl. Acids Res. 31: 3537-3539.

  • V. Solovyev and I. Shahmuradov
    PromH: promoters identification using orthologous genomic sequences
    Nucl. Acids Res. 31: 3540-3545.

  • Allen Chong, Guanglan Zhang, and Vladimir B. Bajic
    FIE2: a program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes
    Nucl. Acids Res. 31: 3546-3553.

  • Anason S. Halees, Dmitriy Leyfer, and Zhiping Weng
    PromoSer: a large-scale mammalian promoter and transcription start site identification service
    Nucl. Acids Res. 31: 3554-3559.

  • Vladimir B. Bajic and Seng Hong Seah
    Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes
    Nucl. Acids Res. 31: 3560-3563.

  • Anton Nekrutenko, Wen-Yu Chung, and Wen-Hsiung Li
    ETOPE: evolutionary test of predicted exons
    Nucl. Acids Res. 31: 3564-3567.

  • Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang, and Adrian R. Krainer
    ESEfinder: a web resource to identify exonic splicing enhancers
    Nucl. Acids Res. 31: 3568-3571.

  • Paul E. Boardman, Stephen G. Oliver, and Simon J. Hubbard
    SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences
    Nucl. Acids Res. 31: 3572-3575.

  • A.E. Kel, E. Gößling, I. Reuter, E. Cheremushkin, O.V. Kel-Margoulis, and E. Wingender
    MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
    Nucl. Acids Res. 31: 3576-3579.

  • William Thompson, Eric C. Rouchka, and Charles E. Lawrence
    Gibbs Recursive Sampler: finding transcription factor binding sites
    Nucl. Acids Res. 31: 3580-3585.

  • Saurabh Sinha and Martin Tompa
    YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
    Nucl. Acids Res. 31: 3586-3588.

  • Alona Sosinsky, Christopher P. Bonin, Richard S. Mann, and Barry Honig
    Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors
    Nucl. Acids Res. 31: 3589-3592.

  • Jacques van Helden
    Regulatory Sequence Analysis Tools
    Nucl. Acids Res. 31: 3593-3596.

  • Shannon D. Schlueter, Qunfeng Dong, and Volker Brendel
    GeneSeqer@PlantGDB: gene structure prediction in plant genomes
    Nucl. Acids Res. 31: 3597-3600.

  • William H. Majoros, Mihaela Pertea, Corina Antonescu, and Steven L. Salzberg
    GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders
    Nucl. Acids Res. 31: 3601-3604.

  • Vladimir B. Bajic, Sin Lam Tan, Allen Chong, Suisheng Tang, Anders Ström, Jan-Åke Gustafsson, Chin-Yo Lin, and Edison T. Liu
    Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes
    Nucl. Acids Res. 31: 3605-3607.

  • Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà, and Graziano Pesole
    PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences
    Nucl. Acids Res. 31: 3608-3612.

  • Jennifer L. Gardy, Cory Spencer, Ke Wang, Martin Ester, Gábor E. Tusnády, István Simon, Sujun Hua, Katalin deFays, Christophe Lambert, Kenta Nakai, and Fiona S.L. Brinkman
    PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria
    Nucl. Acids Res. 31: 3613-3617.

  • Giovanna Ambrosini, Viviane Praz, Vidhya Jagannathan, and Philipp Bucher
    Signal search analysis server
    Nucl. Acids Res. 31: 3618-3620.

  • Pingping Guan, Irini A. Doytchinova, Christianna Zygouri, and Darren R. Flower
    MHCPred: a server for quantitative prediction of peptide–MHC binding
    Nucl. Acids Res. 31: 3621-3624.

  • Pål Puntervoll, Rune Linding, Christine Gemünd, Sophie Chabanis-Davidson, Morten Mattingsdal, Scott Cameron, David M. A. Martin, Gabriele Ausiello, Barbara Brannetti, Anna Costantini, Fabrizio Ferrè, Vincenza Maselli, Allegra Via, Gianni Cesareni, Francesca Diella, Giulio Superti-Furga, Lucjan Wyrwicz, Chenna Ramu, Caroline McGuigan, Rambabu Gudavalli, Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N. Hunter, Rein Aasland, and Toby J. Gibson
    ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
    Nucl. Acids Res. 31: 3625-3630.

  • Frank Eisenhaber, Birgit Eisenhaber, Werner Kubina, Sebastian Maurer-Stroh, Georg Neuberger, Georg Schneider, and Michael Wildpaner
    Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-{Pi}, NMT and PTS1
    Nucl. Acids Res. 31: 3631-3634.

  • John C. Obenauer, Lewis C. Cantley, and Michael B. Yaffe
    Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
    Nucl. Acids Res. 31: 3635-3641.

  • Andrew Kernytsky and Burkhard Rost
    Static benchmarking of membrane helix predictions
    Nucl. Acids Res. 31: 3642-3644.

  • Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt, and Tetsuo Shibuya
    The web server of IBM's Bioinformatics and Pattern Discovery group
    Nucl. Acids Res. 31: 3645-3650.

  • Domènec Farré, Romà Roset, Mario Huerta, José E. Adsuara, Llorenç Roselló, M. Mar Albà, and Xavier Messeguer
    Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN
    Nucl. Acids Res. 31: 3651-3653.

  • Gitanjali Yadav, Rajesh S. Gokhale, and Debasisa Mohanty
    SEARCHPKS: a program for detection and analysis of polyketide synthase domains
    Nucl. Acids Res. 31: 3654-3658.

  • Guojun Yang and Timothy C. Hall
    MAK, a computational tool kit for automated MITE analysis
    Nucl. Acids Res. 31: 3659-3665.

  • Martin C. Frith, Michael C. Li, and Zhiping Weng
    Cluster-Buster: finding dense clusters of motifs in DNA sequences
    Nucl. Acids Res. 31: 3666-3668.

  • David Robelin, Hugues Richard, and Bernard Prum
    SIC: a tool to detect short inverted segments in a biological sequence
    Nucl. Acids Res. 31: 3669-3671.

  • Roman Kolpakov, Ghizlane Bana, and Gregory Kucherov
    mreps: efficient and flexible detection of tandem repeats in DNA
    Nucl. Acids Res. 31: 3672-3678.

  • H. Richard and G. Nuel
    SPA: simple web tool to assess statistical significance of DNA patterns
    Nucl. Acids Res. 31: 3679-3681.

  • Moshe Gal, Tzvi Katz, Amir Ovadia, and Gad Yagil
    TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts
    Nucl. Acids Res. 31: 3682-3685.

  • Kristian Vlahovicek, László Kaján, and Sándor Pongor
    DNA analysis servers:,, and IS
    Nucl. Acids Res. 31: 3686-3687.

  • Tamas Vincze, Janos Posfai, and Richard J. Roberts
    NEBcutter: a program to cleave DNA with restriction enzymes
    Nucl. Acids Res. 31: 3688-3691.

  • C.Z. Cai, L.Y. Han, Z.L. Ji, X. Chen, and Y.Z. Chen
    SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence
    Nucl. Acids Res. 31: 3692-3697.

  • Paul D. Taylor, Teresa K. Attwood, and Darren R. Flower
    BPROMPT: a consensus server for membrane protein prediction
    Nucl. Acids Res. 31: 3698-3700.

  • Rune Linding, Robert B. Russell, Victor Neduva, and Toby J. Gibson
    GlobPlot: exploring protein sequences for globularity and disorder
    Nucl. Acids Res. 31: 3701-3708.

  • Barbara Brannetti and Manuela Helmer-Citterich
    iSPOT: a web tool to infer the interaction specificity of families of protein modules
    Nucl. Acids Res. 31: 3709-3711.

  • Steffen Hennig, Detlef Groth, and Hans Lehrach
    Automated Gene Ontology annotation for anonymous sequence data
    Nucl. Acids Res. 31: 3712-3715.

  • Agnes Hotz-Wagenblatt, Thomas Hankeln, Peter Ernst, Karl-Heinz Glatting, Erwin R. Schmidt, and Sándor Suhai
    ESTAnnotator: a tool for high throughput EST annotation
    Nucl. Acids Res. 31: 3716-3719.

  • François Enault, Karsten Suhre, Olivier Poirot, Chantal Abergel, and Jean-Michel Claverie
    Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes
    Nucl. Acids Res. 31: 3720-3722.

  • Stéphanie Bocs, Stéphane Cruveiller, David Vallenet, Grégory Nuel, and Claudine Médigue
    AMIGene: Annotation of MIcrobial Genes
    Nucl. Acids Res. 31: 3723-3726.

  • Hideaki Sugawara and Satoru Miyazaki
    AHMII: Agent to Help Microbial Information Integration
    Nucl. Acids Res. 31: 3727-3728.

  • Chunyu Liu, Tom I. Bonner, Tu Nguyen, Jennifer L. Lyons, Susan L. Christian, and Elliot S. Gershon
    DNannotator: annotation software tool kit for regional genomic sequences
    Nucl. Acids Res. 31: 3729-3735.

  • Jason McDermott and Ram Samudrala
    Bioverse: functional, structural and contextual annotation of proteins and proteomes
    Nucl. Acids Res. 31: 3736-3737.

  • Thomas Schiex, Jérôme Gouzy, Annick Moisan, and Yannick de Oliveira
    FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
    Nucl. Acids Res. 31: 3738-3741.

  • Sylvain Foissac, Philippe Bardou, Annick Moisan, Marie-Josée Cros, and Thomas Schiex
    EUNE'HOM: a generic similarity-based gene finder using multiple homologous sequences
    Nucl. Acids Res. 31: 3742-3745.

  • Scott J. Emrich, Mary Lowe, and Arthur L. Delcher
    PROBEmer: a web-based software tool for selecting optimal DNA oligos
    Nucl. Acids Res. 31: 3746-3750.

  • S.H. Chen, C.Y. Lin, C.S. Cho, C.Z. Lo, and C.A. Hsiung
    Primer Design Assistant (PDA): a web-based primer design tool
    Nucl. Acids Res. 31: 3751-3754.

  • Guoqing Lu, Michael Hallett, Stephanie Pollock, and David Thomas
    DePIE: Designing Primers for Protein Interaction Experiments
    Nucl. Acids Res. 31: 3755-3757.

  • Niels Tolstrup, Peter S. Nielsen, Jens G. Kolberg, Annett M. Frankel, Henrik Vissing, and Sakari Kauppinen
    OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling
    Nucl. Acids Res. 31: 3758-3762.

  • Timothy Rose, Jorja Henikoff, and Steven Henikoff
    CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design
    Nucl. Acids Res. 31: 3763-3766.

  • Alexander Sczyrba, Jan Krüger, Henning Mersch, Stefan Kurtz, and Robert Giegerich
    RNA-related tools on the Bielefeld Bioinformatics Server
    Nucl. Acids Res. 31: 3767-3770.

  • Chenna Ramu
    SIRW: a web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches
    Nucl. Acids Res. 31: 3771-3774.

  • Sorin Draghici, Purvesh Khatri, Pratik Bhavsar, Abhik Shah, Stephen A. Krawetz, and Michael A. Tainsky
    Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
    Nucl. Acids Res. 31: 3775-3781.

  • Laurent Falquet, Lorenza Bordoli, Vassilios Ioannidis, Marco Pagni, and C. Victor Jongeneel
    Swiss EMBnet node web server
    Nucl. Acids Res. 31: 3782-3783.

  • Elisabeth Gasteiger, Alexandre Gattiker, Christine Hoogland, Ivan Ivanyi, Ron D. Appel, and Amos Bairoch
    ExPASy: the proteomics server for in-depth protein knowledge and analysis
    Nucl. Acids Res. 31: 3784-3788.

  • Sven Mika and Burkhard Rost
    UniqueProt: creating representative protein sequence sets
    Nucl. Acids Res. 31: 3789-3791.

  • Konstantinos Bimpikis, Aidan Budd, Rune Linding, and Toby J. Gibson
    BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases
    Nucl. Acids Res. 31: 3792-3794.

  • Rodrigo Lopez, Ville Silventoinen, Stephen Robinson, Asif Kibria, and Warren Gish
    WU-Blast2 server at the European Bioinformatics Institute
    Nucl. Acids Res. 31: 3795-3798.

  • Günther Zehetner
    OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms
    Nucl. Acids Res. 31: 3799-3803.

  • Krzysztof Ginalski, Jakub Pas, Lucjan S. Wyrwicz, Marcin von Grotthuss, Janusz M. Bujnicki, and Leszek Rychlewski
    ORFeus: detection of distant homology using sequence profiles and predicted secondary structure
    Nucl. Acids Res. 31: 3804-3807.

  • Nicholas E. Taylor and Elizabeth A. Greene
    PARSESNP: a tool for the analysis of nucleotide polymorphisms
    Nucl. Acids Res. 31: 3808-3811.

  • Pauline C. Ng and Steven Henikoff
    SIFT: predicting amino acid changes that affect protein function
    Nucl. Acids Res. 31: 3812-3814.

  • Guillaume Albini, Matthieu Falque, and Johann Joets
    ActionMap: a web-based software that automates loci assignments to framework maps
    Nucl. Acids Res. 31: 3815-3818.

  • Yanlin Huang and David Kowalski
    WEB-THERMODYN: sequence analysis software for profiling DNA helical stability
    Nucl. Acids Res. 31: 3819-3821.

  • I. Q. H. Phan, S. F. Pilbout, W. Fleischmann, and A. Bairoch
    NEWT, a new taxonomy portal
    Nucl. Acids Res. 31: 3822-3823.

  • Michal Lapidot and Yitzhak Pilpel
    Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription
    Nucl. Acids Res. 31: 3824-3828.

  • Frédéric Plewniak, Laurent Bianchetti, Yann Brelivet, Annaick Carles, Frédéric Chalmel, Odile Lecompte, Thiebaut Mochel, Luc Moulinier, Arnaud Muller, Jean Muller, Veronique Prigent, Raymond Ripp, Jean-Claude Thierry, Julie D. Thompson, Nicolas Wicker, and Olivier Poch
    PipeAlign: a new toolkit for protein family analysis
    Nucl. Acids Res. 31: 3829-3832.

  • Jinfeng Liu and Burkhard Rost
    NORSp: predictions of long regions without regular secondary structure
    Nucl. Acids Res. 31: 3833-3835.

  • H. Sugawara and S. Miyazaki
    Biological SOAP servers and web services provided by the public sequence data bank
    Nucl. Acids Res. 31: 3836-3839.

  • Mathieu Blanchette and Martin Tompa
    FootPrinter: a program designed for phylogenetic footprinting
    Nucl. Acids Res. 31: 3840-3842.

  • Edouard Yeramian and Louis Jones
    GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives
    Nucl. Acids Res. 31: 3843-3849.

  • Niko Beerenwinkel, Martin Däumer, Mark Oette, Klaus Korn, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, Joachim Selbig, and Hauke Walter
    Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
    Nucl. Acids Res. 31: 3850-3855.

  • Lucy Skrabanek, Fabien Campagne, and Harel Weinstein
    Building protein diagrams on the web with the residue-based diagram editor RbDe
    Nucl. Acids Res. 31: 3856-3858.

  • Aaron J. Mackey, Timothy A.J. Haystead, and William R. Pearson
    CRP: Cleavage of Radiolabeled Phosphoproteins
    Nucl. Acids Res. 31: 3859-3861.

  • Karsten Hiller, Max Schobert, Claudia Hundertmark, Dieter Jahn, and Richard Münch
    JVirGel: calculation of virtual two-dimensional protein gels
    Nucl. Acids Res. 31: 3862-3865.

  • Carolina Perez-Iratxeta, Antonio Pérez, Peer Bork, and Miguel Andrade
    Update on XplorMed: a web server for exploring scientific literature
    Nucl. Acids Res. 31: 3866-3868.


Latest update: October 1, 2004

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)
Please replace (at) by @.

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