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Volume 31(13);  July 1, 2003
Articles
Editorial
Nucleic Acids Res. 2003 July 1; 31(13): 3289.
PMCID: PMC169037
Detection of reliable and unexpected protein fold predictions using 3D-Jury
Krzysztof Ginalski and Leszek Rychlewski
Nucleic Acids Res. 2003 July 1; 31(13): 3291–3292.
PMCID: PMC168910
DSSPcont: continuous secondary structure assignments for proteins
Phil Carter, Claus A. F. Andersen, and Burkhard Rost
Nucleic Acids Res. 2003 July 1; 31(13): 3293–3295.
PMCID: PMC169032
PROTINFO: secondary and tertiary protein structure prediction
Ling-Hong Hung and Ram Samudrala
Nucleic Acids Res. 2003 July 1; 31(13): 3296–3299.
PMCID: PMC168948
The PredictProtein server
Burkhard Rost and Jinfeng Liu
Nucleic Acids Res. 2003 July 1; 31(13): 3300–3304.
PMCID: PMC168915
GeneSilico protein structure prediction meta-server
Michal A. Kurowski and Janusz M. Bujnicki
Nucleic Acids Res. 2003 July 1; 31(13): 3305–3307.
PMCID: PMC168964
META-PP: single interface to crucial prediction servers
Volker A. Eyrich and Burkhard Rost
Nucleic Acids Res. 2003 July 1; 31(13): 3308–3310.
PMCID: PMC168978
EVA: evaluation of protein structure prediction servers
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
Nucleic Acids Res. 2003 July 1; 31(13): 3311–3315.
PMCID: PMC169025
VADAR: a web server for quantitative evaluation of protein structure quality
Leigh Willard, Anuj Ranjan, Haiyan Zhang, Hassan Monzavi, Robert F. Boyko, Brian D. Sykes, and David S. Wishart
Nucleic Acids Res. 2003 July 1; 31(13): 3316–3319.
PMCID: PMC168972
ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins
Patrice Gouet, Xavier Robert, and Emmanuel Courcelle
Nucleic Acids Res. 2003 July 1; 31(13): 3320–3323.
PMCID: PMC168963
WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures
Mike P. Liang, D. Rey Banatao, Teri E. Klein, Douglas L. Brutlag, and Russ B. Altman
Nucleic Acids Res. 2003 July 1; 31(13): 3324–3327.
PMCID: PMC168960
3matrix and 3motif: a protein structure visualization system for conserved sequence motifs
Steven P. Bennett, Lin Lu, and Douglas L. Brutlag
Nucleic Acids Res. 2003 July 1; 31(13): 3328–3332.
PMCID: PMC168971
Motif3D: relating protein sequence motifs to 3D structure
Anna Gaulton and Teresa K. Attwood
Nucleic Acids Res. 2003 July 1; 31(13): 3333–3336.
PMCID: PMC168941
LOC3D: annotate sub-cellular localization for protein structures
Rajesh Nair and Burkhard Rost
Nucleic Acids Res. 2003 July 1; 31(13): 3337–3340.
PMCID: PMC168921
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
Alexander Stark and Robert B. Russell
Nucleic Acids Res. 2003 July 1; 31(13): 3341–3344.
PMCID: PMC168913
NCI: a server to identify non-canonical interactions in protein structures
M. Madan Babu
Nucleic Acids Res. 2003 July 1; 31(13): 3345–3348.
PMCID: PMC168935
MolSurfer: a macromolecular interface navigator
Razif R. Gabdoulline, Rebecca C. Wade, and Dirk Walther
Nucleic Acids Res. 2003 July 1; 31(13): 3349–3351.
PMCID: PMC168994
CASTp: Computed Atlas of Surface Topography of proteins
T. Andrew Binkowski, Shapor Naghibzadeh, and Jie Liang
Nucleic Acids Res. 2003 July 1; 31(13): 3352–3355.
PMCID: PMC168919
SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules
A. S. Z. Hussain, Ch. Kiran Kumar, C. K. Rajesh, S. S. Sheik, and K. Sekar
Nucleic Acids Res. 2003 July 1; 31(13): 3356–3358.
PMCID: PMC168993
Servers for sequence–structure relationship analysis and prediction
Zsuzsanna Dosztányi, Csaba Magyar, Gábor E. Tusnády, Miklós Cserző, András Fiser, and István Simon
Nucleic Acids Res. 2003 July 1; 31(13): 3359–3363.
PMCID: PMC168995
POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level
Luigi Cavallo, Jens Kleinjung, and Franca Fraternali
Nucleic Acids Res. 2003 July 1; 31(13): 3364–3366.
PMCID: PMC169007
MATRAS: a program for protein 3D structure comparison
Takeshi Kawabata
Nucleic Acids Res. 2003 July 1; 31(13): 3367–3369.
PMCID: PMC168987
LGA: a method for finding 3D similarities in protein structures
Adam Zemla
Nucleic Acids Res. 2003 July 1; 31(13): 3370–3374.
PMCID: PMC168977
Tools for comparative protein structure modeling and analysis
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
Nucleic Acids Res. 2003 July 1; 31(13): 3375–3380.
PMCID: PMC168950
SWISS-MODEL: an automated protein homology-modeling server
Torsten Schwede, Jürgen Kopp, Nicolas Guex, and Manuel C. Peitsch
Nucleic Acids Res. 2003 July 1; 31(13): 3381–3385.
PMCID: PMC168927
STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence
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
Nucleic Acids Res. 2003 July 1; 31(13): 3386–3392.
PMCID: PMC168984
Integrated databanks access and sequence/structure analysis services at the PBIL
Guy Perrière, Christophe Combet, Simon Penel, Christophe Blanchet, Jean Thioulouse, Christophe Geourjon, Julien Grassot, Céline Charavay, Manolo Gouy, Laurent Duret, and Gilbert Deléage
Nucleic Acids Res. 2003 July 1; 31(13): 3393–3399.
PMCID: PMC168937
NRSAS: Nuclear Receptor Structure Analysis Servers
Emmanuel Bettler, Roland Krause, Florence Horn, and Gert Vriend
Nucleic Acids Res. 2003 July 1; 31(13): 3400–3403.
PMCID: PMC168912
SSEP: secondary structural elements of proteins
V. Shanthi, P. Selvarani, Ch. Kiran Kumar, C. S. Mohire, and K. Sekar
Nucleic Acids Res. 2003 July 1; 31(13): 3404–3405.
PMCID: PMC168914
Mfold web server for nucleic acid folding and hybridization prediction
Michael Zuker
Nucleic Acids Res. 2003 July 1; 31(13): 3406–3415.
PMCID: PMC169194
RNAsoft: a suite of RNA secondary structure prediction and design software tools
Mirela Andronescu, Rosalía Aguirre-Hernández, Anne Condon, and Holger H. Hoos
Nucleic Acids Res. 2003 July 1; 31(13): 3416–3422.
PMCID: PMC169018
Pfold: RNA secondary structure prediction using stochastic context-free grammars
Bjarne Knudsen and Jotun Hein
Nucleic Acids Res. 2003 July 1; 31(13): 3423–3428.
PMCID: PMC169020
Vienna RNA secondary structure server
Ivo L. Hofacker
Nucleic Acids Res. 2003 July 1; 31(13): 3429–3431.
PMCID: PMC169005
PseudoViewer2: visualization of RNA pseudoknots of any type
Kyungsook Han and Yanga Byun
Nucleic Acids Res. 2003 July 1; 31(13): 3432–3440.
PMCID: PMC168946
A software tool-box for analysis of regulatory RNA elements
Peter Bengert and Thomas Dandekar
Nucleic Acids Res. 2003 July 1; 31(13): 3441–3445.
PMCID: PMC168974
GPRM: a genetic programming approach to finding common RNA secondary structure elements
Yuh-Jyh Hu
Nucleic Acids Res. 2003 July 1; 31(13): 3446–3449.
PMCID: PMC168928
Tools for the automatic identification and classification of RNA base pairs
Huanwang Yang, Fabrice Jossinet, Neocles Leontis, Li Chen, John Westbrook, Helen Berman, and Eric Westhof
Nucleic Acids Res. 2003 July 1; 31(13): 3450–3460.
PMCID: PMC168936
GEPAS: a web-based resource for microarray gene expression data analysis
Javier Herrero, Fátima Al-Shahrour, Ramón Díaz-Uriarte, Álvaro Mateos, Juan M. Vaquerizas, Javier Santoyo, and Joaquín Dopazo
Nucleic Acids Res. 2003 July 1; 31(13): 3461–3467.
PMCID: PMC168997
INCLUSive: a web portal and service registry for microarray and regulatory sequence analysis
Bert Coessens, Gert Thijs, Stein Aerts, Kathleen Marchal, Frank De Smet, Kristof Engelen, Patrick Glenisson, Yves Moreau, Janick Mathys, and Bart De Moor
Nucleic Acids Res. 2003 July 1; 31(13): 3468–3470.
PMCID: PMC169021
GenePublisher: automated analysis of DNA microarray data
Steen Knudsen, Christopher Workman, Thomas Sicheritz-Ponten, and Carsten Friis
Nucleic Acids Res. 2003 July 1; 31(13): 3471–3476.
PMCID: PMC169191
ExpressYourself: a modular platform for processing and visualizing microarray data
Nicholas M. Luscombe, Thomas E. Royce, Paul Bertone, Nathaniel Echols, Christine E. Horak, Joseph T. Chang, Michael Snyder, and Mark Gerstein
Nucleic Acids Res. 2003 July 1; 31(13): 3477–3482.
PMCID: PMC169034
ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis
Sheng Zhong, Cheng Li, and Wing Hung Wong
Nucleic Acids Res. 2003 July 1; 31(13): 3483–3486.
PMCID: PMC169004
REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
Crispin Roven and Harmen J. Bussemaker
Nucleic Acids Res. 2003 July 1; 31(13): 3487–3490.
PMCID: PMC169192
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
Henrik Bjørn Nielsen, Rasmus Wernersson, and Steen Knudsen
Nucleic Acids Res. 2003 July 1; 31(13): 3491–3496.
PMCID: PMC169028
Multiple sequence alignment with the Clustal series of programs
Ramu Chenna, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, and Julie D. Thompson
Nucleic Acids Res. 2003 July 1; 31(13): 3497–3500.
PMCID: PMC168907
CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics
Davinder K. Kohli and Anand K. Bachhawat
Nucleic Acids Res. 2003 July 1; 31(13): 3501–3502.
PMCID: PMC168909
Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments
Olivier Poirot, Eamonn O'Toole, and Cedric Notredame
Nucleic Acids Res. 2003 July 1; 31(13): 3503–3506.
PMCID: PMC168929
SLAM web server for comparative gene finding and alignment
Simon Cawley, Lior Pachter, and Marina Alexandersson
Nucleic Acids Res. 2003 July 1; 31(13): 3507–3509.
PMCID: PMC168989
Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence
Yvonne J. K. Edwards, Tim J. Carver, Tanya Vavouri, Martin Frith, Martin J. Bishop, and Greg Elgar
Nucleic Acids Res. 2003 July 1; 31(13): 3510–3517.
PMCID: PMC168908
MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences
Scott Schwartz, Laura Elnitski, Mei Li, Matt Weirauch, Cathy Riemer, Arian Smit, Eric D. Green, Ross C. Hardison, and Webb Miller
Nucleic Acids Res. 2003 July 1; 31(13): 3518–3524.
PMCID: PMC168985
MAVID multiple alignment server
Nicolas Bray and Lior Pachter
Nucleic Acids Res. 2003 July 1; 31(13): 3525–3526.
PMCID: PMC169029
EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae
Liliana Florea, Michael McClelland, Cathy Riemer, Scott Schwartz, and Webb Miller
Nucleic Acids Res. 2003 July 1; 31(13): 3527–3532.
PMCID: PMC168958
MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences
Bernett T. K. Lee, Tin Wee Tan, and Shoba Ranganathan
Nucleic Acids Res. 2003 July 1; 31(13): 3533–3536.
PMCID: PMC168968
RevTrans: multiple alignment of coding DNA from aligned amino acid sequences
Rasmus Wernersson and Anders Gorm Pedersen
Nucleic Acids Res. 2003 July 1; 31(13): 3537–3539.
PMCID: PMC169015
PromH: promoters identification using orthologous genomic sequences
V. V. Solovyev and I. A. Shahmuradov
Nucleic Acids Res. 2003 July 1; 31(13): 3540–3545.
PMCID: PMC168932
FIE2: a program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes
Allen Chong, Guanglan Zhang, and Vladimir B. Bajic
Nucleic Acids Res. 2003 July 1; 31(13): 3546–3553.
PMCID: PMC169010
PromoSer: a large-scale mammalian promoter and transcription start site identification service
Anason S. Halees, Dmitriy Leyfer, and Zhiping Weng
Nucleic Acids Res. 2003 July 1; 31(13): 3554–3559.
PMCID: PMC168956
Dragon Gene Start Finder identifies approximate locations of the 5′ ends of genes
Vladimir B. Bajic and Seng Hong Seah
Nucleic Acids Res. 2003 July 1; 31(13): 3560–3563.
PMCID: PMC168976
ETOPE: evolutionary test of predicted exons
Anton Nekrutenko, Wen-Yu Chung, and Wen-Hsiung Li
Nucleic Acids Res. 2003 July 1; 31(13): 3564–3567.
PMCID: PMC169003
ESEfinder: a web resource to identify exonic splicing enhancers
Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang, and Adrian R. Krainer
Nucleic Acids Res. 2003 July 1; 31(13): 3568–3571.
PMCID: PMC169022
SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences
Paul E. Boardman, Stephen G. Oliver, and Simon J. Hubbard
Nucleic Acids Res. 2003 July 1; 31(13): 3572–3575.
PMCID: PMC168918
MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
A.E. Kel, E. Gößling, I. Reuter, E. Cheremushkin, O.V. Kel-Margoulis, and E. Wingender
Nucleic Acids Res. 2003 July 1; 31(13): 3576–3579.
PMCID: PMC169193
Gibbs Recursive Sampler: finding transcription factor binding sites
William Thompson, Eric C. Rouchka, and Charles E. Lawrence
Nucleic Acids Res. 2003 July 1; 31(13): 3580–3585.
PMCID: PMC169014
YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
Saurabh Sinha and Martin Tompa
Nucleic Acids Res. 2003 July 1; 31(13): 3586–3588.
PMCID: PMC169024
Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors
Alona Sosinsky, Christopher P. Bonin, Richard S. Mann, and Barry Honig
Nucleic Acids Res. 2003 July 1; 31(13): 3589–3592.
PMCID: PMC168951
Regulatory Sequence Analysis Tools
Jacques van Helden
Nucleic Acids Res. 2003 July 1; 31(13): 3593–3596.
PMCID: PMC168973
GeneSeqer@PlantGDB: gene structure prediction in plant genomes
Shannon D. Schlueter, Qunfeng Dong, and Volker Brendel
Nucleic Acids Res. 2003 July 1; 31(13): 3597–3600.
PMCID: PMC168940
GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders
William H. Majoros, Mihaela Pertea, Corina Antonescu, and Steven L. Salzberg
Nucleic Acids Res. 2003 July 1; 31(13): 3601–3604.
PMCID: PMC168934
Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes
Vladimir B. Bajic, Sin Lam Tan, Allen Chong, Suisheng Tang, Anders Ström, Jan-Åke Gustafsson, Chin-Yo Lin, and Edison T. Liu
Nucleic Acids Res. 2003 July 1; 31(13): 3605–3607.
PMCID: PMC168924
PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences
Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà, and Graziano Pesole
Nucleic Acids Res. 2003 July 1; 31(13): 3608–3612.
PMCID: PMC168955
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria
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
Nucleic Acids Res. 2003 July 1; 31(13): 3613–3617.
PMCID: PMC169008
Signal search analysis server
Giovanna Ambrosini, Viviane Praz, Vidhya Jagannathan, and Philipp Bucher
Nucleic Acids Res. 2003 July 1; 31(13): 3618–3620.
PMCID: PMC169017
MHCPred: a server for quantitative prediction of peptide–MHC binding
Pingping Guan, Irini A. Doytchinova, Christianna Zygouri, and Darren R. Flower
Nucleic Acids Res. 2003 July 1; 31(13): 3621–3624.
PMCID: PMC168917
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
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
Nucleic Acids Res. 2003 July 1; 31(13): 3625–3630.
PMCID: PMC168952
Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Π, NMT and PTS1
Frank Eisenhaber, Birgit Eisenhaber, Werner Kubina, Sebastian Maurer-Stroh, Georg Neuberger, Georg Schneider, and Michael Wildpaner
Nucleic Acids Res. 2003 July 1; 31(13): 3631–3634.
PMCID: PMC168944
Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs
John C. Obenauer, Lewis C. Cantley, and Michael B. Yaffe
Nucleic Acids Res. 2003 July 1; 31(13): 3635–3641.
PMCID: PMC168990
Static benchmarking of membrane helix predictions
Andrew Kernytsky and Burkhard Rost
Nucleic Acids Res. 2003 July 1; 31(13): 3642–3644.
PMCID: PMC168939
The web server of IBM's Bioinformatics and Pattern Discovery group
Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt, and Tetsuo Shibuya
Nucleic Acids Res. 2003 July 1; 31(13): 3645–3650.
PMCID: PMC169027
Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN
Domènec Farré, Romà Roset, Mario Huerta, José E. Adsuara, Llorenç Roselló, M. Mar Albà, and Xavier Messeguer
Nucleic Acids Res. 2003 July 1; 31(13): 3651–3653.
PMCID: PMC169011
SEARCHPKS: a program for detection and analysis of polyketide synthase domains
Gitanjali Yadav, Rajesh S. Gokhale, and Debasisa Mohanty
Nucleic Acids Res. 2003 July 1; 31(13): 3654–3658.
PMCID: PMC169013
MAK, a computational tool kit for automated MITE analysis
Guojun Yang and Timothy C. Hall
Nucleic Acids Res. 2003 July 1; 31(13): 3659–3665.
PMCID: PMC168938
Cluster-Buster: finding dense clusters of motifs in DNA sequences
Martin C. Frith, Michael C. Li, and Zhiping Weng
Nucleic Acids Res. 2003 July 1; 31(13): 3666–3668.
PMCID: PMC168947
SIC: a tool to detect short inverted segments in a biological sequence
David Robelin, Hugues Richard, and Bernard Prum
Nucleic Acids Res. 2003 July 1; 31(13): 3669–3671.
PMCID: PMC169195
mreps: efficient and flexible detection of tandem repeats in DNA
Roman Kolpakov, Ghizlane Bana, and Gregory Kucherov
Nucleic Acids Res. 2003 July 1; 31(13): 3672–3678.
PMCID: PMC169196
SPA: simple web tool to assess statistical significance of DNA patterns
H. Richard and G. Nuel
Nucleic Acids Res. 2003 July 1; 31(13): 3679–3681.
PMCID: PMC169190
TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts
Moshe Gal, Tzvi Katz, Amir Ovadia, and Gad Yagil
Nucleic Acids Res. 2003 July 1; 31(13): 3682–3685.
PMCID: PMC169031
DNA analysis servers: plot.it, bend.it, model.it and IS
Kristian Vlahoviček, László Kaján, and Sándor Pongor
Nucleic Acids Res. 2003 July 1; 31(13): 3686–3687.
PMCID: PMC168966
NEBcutter: a program to cleave DNA with restriction enzymes
Tamas Vincze, Janos Posfai, and Richard J. Roberts
Nucleic Acids Res. 2003 July 1; 31(13): 3688–3691.
PMCID: PMC168933
SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence
C.Z. Cai, L.Y. Han, Z.L. Ji, X. Chen, and Y.Z. Chen
Nucleic Acids Res. 2003 July 1; 31(13): 3692–3697.
PMCID: PMC169006
BPROMPT: a consensus server for membrane protein prediction
Paul D. Taylor, Teresa K. Attwood, and Darren R. Flower
Nucleic Acids Res. 2003 July 1; 31(13): 3698–3700.
PMCID: PMC168961
GlobPlot: exploring protein sequences for globularity and disorder
Rune Linding, Robert B. Russell, Victor Neduva, and Toby J. Gibson
Nucleic Acids Res. 2003 July 1; 31(13): 3701–3708.
PMCID: PMC169197
iSPOT: a web tool to infer the interaction specificity of families of protein modules
Barbara Brannetti and Manuela Helmer-Citterich
Nucleic Acids Res. 2003 July 1; 31(13): 3709–3711.
PMCID: PMC168998
Automated Gene Ontology annotation for anonymous sequence data
Steffen Hennig, Detlef Groth, and Hans Lehrach
Nucleic Acids Res. 2003 July 1; 31(13): 3712–3715.
PMCID: PMC168988
ESTAnnotator: a tool for high throughput EST annotation
Agnes Hotz-Wagenblatt, Thomas Hankeln, Peter Ernst, Karl-Heinz Glatting, Erwin R. Schmidt, and Sándor Suhai
Nucleic Acids Res. 2003 July 1; 31(13): 3716–3719.
PMCID: PMC169160
Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes
François Enault, Karsten Suhre, Olivier Poirot, Chantal Abergel, and Jean-Michel Claverie
Nucleic Acids Res. 2003 July 1; 31(13): 3720–3722.
PMCID: PMC169009
AMIGene: Annotation of MIcrobial Genes
Stéphanie Bocs, Stéphane Cruveiller, David Vallenet, Grégory Nuel, and Claudine Médigue
Nucleic Acids Res. 2003 July 1; 31(13): 3723–3726.
PMCID: PMC168996
AHMII: Agent to Help Microbial Information Integration
Hideaki Sugawara and Satoru Miyazaki
Nucleic Acids Res. 2003 July 1; 31(13): 3727–3728.
PMCID: PMC168930
DNannotator: annotation software tool kit for regional genomic sequences
Chunyu Liu, Tom I. Bonner, Tu Nguyen, Jennifer L. Lyons, Susan L. Christian, and Elliot S. Gershon
Nucleic Acids Res. 2003 July 1; 31(13): 3729–3735.
PMCID: PMC168949
Bioverse: functional, structural and contextual annotation of proteins and proteomes
Jason McDermott and Ram Samudrala
Nucleic Acids Res. 2003 July 1; 31(13): 3736–3737.
PMCID: PMC168957
FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
Thomas Schiex, Jérôme Gouzy, Annick Moisan, and Yannick de Oliveira
Nucleic Acids Res. 2003 July 1; 31(13): 3738–3741.
PMCID: PMC169016
EUGÈNE'HOM: a generic similarity-based gene finder using multiple homologous sequences
Sylvain Foissac, Philippe Bardou, Annick Moisan, Marie-Josée Cros, and Thomas Schiex
Nucleic Acids Res. 2003 July 1; 31(13): 3742–3745.
PMCID: PMC168992
PROBEmer: a web-based software tool for selecting optimal DNA oligos
Scott J. Emrich, Mary Lowe, and Arthur L. Delcher
Nucleic Acids Res. 2003 July 1; 31(13): 3746–3750.
PMCID: PMC168975
Primer Design Assistant (PDA): a web-based primer design tool
S.H. Chen, C.Y. Lin, C.S. Cho, C.Z. Lo, and C.A. Hsiung
Nucleic Acids Res. 2003 July 1; 31(13): 3751–3754.
PMCID: PMC168967
DePIE: Designing Primers for Protein Interaction Experiments
Guoqing Lu, Michael Hallett, Stephanie Pollock, and David Thomas
Nucleic Acids Res. 2003 July 1; 31(13): 3755–3757.
PMCID: PMC168983
OligoDesign: optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling
Niels Tolstrup, Peter S. Nielsen, Jens G. Kolberg, Annett M. Frankel, Henrik Vissing, and Sakari Kauppinen
Nucleic Acids Res. 2003 July 1; 31(13): 3758–3762.
PMCID: PMC168986
CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design
Timothy M. Rose, Jorja G. Henikoff, and Steven Henikoff
Nucleic Acids Res. 2003 July 1; 31(13): 3763–3766.
PMCID: PMC168931
RNA-related tools on the Bielefeld Bioinformatics Server
Alexander Sczyrba, Jan Krüger, Henning Mersch, Stefan Kurtz, and Robert Giegerich
Nucleic Acids Res. 2003 July 1; 31(13): 3767–3770.
PMCID: PMC168982
SIRW: a web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches
Chenna Ramu
Nucleic Acids Res. 2003 July 1; 31(13): 3771–3774.
PMCID: PMC168953
Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
Sorin Draghici, Purvesh Khatri, Pratik Bhavsar, Abhik Shah, Stephen A. Krawetz, and Michael A. Tainsky
Nucleic Acids Res. 2003 July 1; 31(13): 3775–3781.
PMCID: PMC169030
Swiss EMBnet node web server
Laurent Falquet, Lorenza Bordoli, Vassilios Ioannidis, Marco Pagni, and C. Victor Jongeneel
Nucleic Acids Res. 2003 July 1; 31(13): 3782–3783.
PMCID: PMC168954
ExPASy: the proteomics server for in-depth protein knowledge and analysis
Elisabeth Gasteiger, Alexandre Gattiker, Christine Hoogland, Ivan Ivanyi, Ron D. Appel, and Amos Bairoch
Nucleic Acids Res. 2003 July 1; 31(13): 3784–3788.
PMCID: PMC168970
UniqueProt: creating representative protein sequence sets
Sven Mika and Burkhard Rost
Nucleic Acids Res. 2003 July 1; 31(13): 3789–3791.
PMCID: PMC169026
BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases
Konstantinos Bimpikis, Aidan Budd, Rune Linding, and Toby J. Gibson
Nucleic Acids Res. 2003 July 1; 31(13): 3792–3794.
PMCID: PMC168942
WU-Blast2 server at the European Bioinformatics Institute
Rodrigo Lopez, Ville Silventoinen, Stephen Robinson, Asif Kibria, and Warren Gish
Nucleic Acids Res. 2003 July 1; 31(13): 3795–3798.
PMCID: PMC168979
OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms
Günther Zehetner
Nucleic Acids Res. 2003 July 1; 31(13): 3799–3803.
PMCID: PMC168962
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure
Krzysztof Ginalski, Jakub Pas, Lucjan S. Wyrwicz, Marcin von Grotthuss, Janusz M. Bujnicki, and Leszek Rychlewski
Nucleic Acids Res. 2003 July 1; 31(13): 3804–3807.
PMCID: PMC168911
PARSESNP: a tool for the analysis of nucleotide polymorphisms
Nicholas E. Taylor and Elizabeth A. Greene
Nucleic Acids Res. 2003 July 1; 31(13): 3808–3811.
PMCID: PMC168980
SIFT: predicting amino acid changes that affect protein function
Pauline C. Ng and Steven Henikoff
Nucleic Acids Res. 2003 July 1; 31(13): 3812–3814.
PMCID: PMC168916
ActionMap: a web-based software that automates loci assignments to framework maps
Guillaume Albini, Matthieu Falque, and Johann Joets
Nucleic Acids Res. 2003 July 1; 31(13): 3815–3818.
PMCID: PMC169000
WEB-THERMODYN: sequence analysis software for profiling DNA helical stability
Yanlin Huang and David Kowalski
Nucleic Acids Res. 2003 July 1; 31(13): 3819–3821.
PMCID: PMC168969
NEWT, a new taxonomy portal
I. Q. H. Phan, S. F. Pilbout, W. Fleischmann, and A. Bairoch
Nucleic Acids Res. 2003 July 1; 31(13): 3822–3823.
PMCID: PMC168923
Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription
Michal Lapidot and Yitzhak Pilpel
Nucleic Acids Res. 2003 July 1; 31(13): 3824–3828.
PMCID: PMC168999
PipeAlign: a new toolkit for protein family analysis
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
Nucleic Acids Res. 2003 July 1; 31(13): 3829–3832.
PMCID: PMC168925
NORSp: predictions of long regions without regular secondary structure
Jinfeng Liu and Burkhard Rost
Nucleic Acids Res. 2003 July 1; 31(13): 3833–3835.
PMCID: PMC168922
Biological SOAP servers and web services provided by the public sequence data bank
H. Sugawara and S. Miyazaki
Nucleic Acids Res. 2003 July 1; 31(13): 3836–3839.
PMCID: PMC168965
FootPrinter: a program designed for phylogenetic footprinting
Mathieu Blanchette and Martin Tompa
Nucleic Acids Res. 2003 July 1; 31(13): 3840–3842.
PMCID: PMC169012
GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives
Edouard Yeramian and Louis Jones
Nucleic Acids Res. 2003 July 1; 31(13): 3843–3849.
PMCID: PMC169033
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
Niko Beerenwinkel, Martin Däumer, Mark Oette, Klaus Korn, Daniel Hoffmann, Rolf Kaiser, Thomas Lengauer, Joachim Selbig, and Hauke Walter
Nucleic Acids Res. 2003 July 1; 31(13): 3850–3855.
PMCID: PMC168981
Building protein diagrams on the web with the residue-based diagram editor RbDe
Lucy Skrabanek, Fabien Campagne, and Harel Weinstein
Nucleic Acids Res. 2003 July 1; 31(13): 3856–3858.
PMCID: PMC168959
CRP: Cleavage of Radiolabeled Phosphoproteins
Aaron J. Mackey, Timothy A.J. Haystead, and William R. Pearson
Nucleic Acids Res. 2003 July 1; 31(13): 3859–3861.
PMCID: PMC168920
JVirGel: calculation of virtual two-dimensional protein gels
Karsten Hiller, Max Schobert, Claudia Hundertmark, Dieter Jahn, and Richard Münch
Nucleic Acids Res. 2003 July 1; 31(13): 3862–3865.
PMCID: PMC168943
Update on XplorMed: a web server for exploring scientific literature
Carolina Perez-Iratxeta, Antonio J. Pérez, Peer Bork, and Miguel A. Andrade
Nucleic Acids Res. 2003 July 1; 31(13): 3866–3868.
PMCID: PMC168945
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