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
  MATCH^TM: 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-, 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: plot.it, bend.it, model.it 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
  EUGÈNE'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) gmx.de
Please replace (at) by @.