Nucleic Acids Research

Editorial:

Editorial
Nucl. Acids Res. 2003 31: 3289; doi:10.1093/nar/gkg631 [Extract] [FREE Full Text] [Print PDF] [Request Permissions]  

Articles:

Krzysztof Ginalski and Leszek Rychlewski

Detection of reliable and unexpected protein fold predictions using 3D-Jury
Nucl. Acids Res. 2003 31: 3291-3292; doi:10.1093/nar/gkg503 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Phil Carter, Claus A. F. Andersen, and Burkhard Rost

DSSPcont: continuous secondary structure assignments for proteins
Nucl. Acids Res. 2003 31: 3293-3295; doi:10.1093/nar/gkg626 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Ling-Hong Hung and Ram Samudrala

PROTINFO: secondary and tertiary protein structure prediction
Nucl. Acids Res. 2003 31: 3296-3299; doi:10.1093/nar/gkg541 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Burkhard Rost and Jinfeng Liu

The PredictProtein server
Nucl. Acids Res. 2003 31: 3300-3304; doi:10.1093/nar/gkg508 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michal A. Kurowski and Janusz M. Bujnicki

GeneSilico protein structure prediction meta-server
Nucl. Acids Res. 2003 31: 3305-3307; doi:10.1093/nar/gkg557 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Volker A. Eyrich and Burkhard Rost

META-PP: single interface to crucial prediction servers
Nucl. Acids Res. 2003 31: 3308-3310; doi:10.1093/nar/gkg572 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3311-3315; doi:10.1093/nar/gkg619 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3316-3319; doi:10.1093/nar/gkg565 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Patrice Gouet, Xavier Robert, and Emmanuel Courcelle

ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins
Nucl. Acids Res. 2003 31: 3320-3323; doi:10.1093/nar/gkg556 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3324-3327; doi:10.1093/nar/gkg553 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Steven P. Bennett, Lin Lu, and Douglas L. Brutlag

3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs
Nucl. Acids Res. 2003 31: 3328-3332; doi:10.1093/nar/gkg564 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Anna Gaulton and Teresa K. Attwood

Motif3D: relating protein sequence motifs to 3D structure
Nucl. Acids Res. 2003 31: 3333-3336; doi:10.1093/nar/gkg534 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rajesh Nair and Burkhard Rost

LOC3D: annotate sub-cellular localization for protein structures
Nucl. Acids Res. 2003 31: 3337-3340; doi:10.1093/nar/gkg514 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Alexander Stark and Robert B. Russell

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
Nucl. Acids Res. 2003 31: 3341-3344; doi:10.1093/nar/gkg506 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

M. Madan Babu

NCI: a server to identify non-canonical interactions in protein structures
Nucl. Acids Res. 2003 31: 3345-3348; doi:10.1093/nar/gkg528 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Razif R. Gabdoulline, Rebecca C. Wade, and Dirk Walther

MolSurfer: a macromolecular interface navigator
Nucl. Acids Res. 2003 31: 3349-3351; doi:10.1093/nar/gkg588 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

T. Andrew Binkowski, Shapor Naghibzadeh, and Jie Liang

CASTp: Computed Atlas of Surface Topography of proteins
Nucl. Acids Res. 2003 31: 3352-3355; doi:10.1093/nar/gkg512 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3356-3358; doi:10.1093/nar/gkg587 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3359-3363; doi:10.1093/nar/gkg589 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Luigi Cavallo, Jens Kleinjung, and Franca Fraternali

POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level
Nucl. Acids Res. 2003 31: 3364-3366; doi:10.1093/nar/gkg601 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Takeshi Kawabata

MATRAS: a program for protein 3D structure comparison
Nucl. Acids Res. 2003 31: 3367-3369; doi:10.1093/nar/gkg581 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Adam Zemla

LGA: a method for finding 3D similarities in protein structures
Nucl. Acids Res. 2003 31: 3370-3374; doi:10.1093/nar/gkg571 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3375-3380; doi:10.1093/nar/gkg543 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Torsten Schwede, Jürgen Kopp, Nicolas Guex, and Manuel C. Peitsch

SWISS-MODEL: an automated protein homology-modeling server
Nucl. Acids Res. 2003 31: 3381-3385; doi:10.1093/nar/gkg520 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3386-3392; doi:10.1093/nar/gkg578 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3393-3399; doi:10.1093/nar/gkg530 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Emmanuel Bettler, Roland Krause, Florence Horn, and Gert Vriend

NRSAS: Nuclear Receptor Structure Analysis Servers
Nucl. Acids Res. 2003 31: 3400-3403; doi:10.1093/nar/gkg505 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

V. Shanthi, P. Selvarani, Ch. Kiran Kumar, C. S. Mohire, and K. Sekar

SSEP: secondary structural elements of proteins
Nucl. Acids Res. 2003 31: 3404-3405; doi:10.1093/nar/gkg507 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Michael Zuker

Mfold web server for nucleic acid folding and hybridization prediction
Nucl. Acids Res. 2003 31: 3406-3415; doi:10.1093/nar/gkg595 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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. 2003 31: 3416-3422; doi:10.1093/nar/gkg612 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Bjarne Knudsen and Jotun Hein

Pfold: RNA secondary structure prediction using stochastic context-free grammars
Nucl. Acids Res. 2003 31: 3423-3428; doi:10.1093/nar/gkg614 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Ivo L. Hofacker

Vienna RNA secondary structure server
Nucl. Acids Res. 2003 31: 3429-3431; doi:10.1093/nar/gkg599 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kyungsook Han and Yanga Byun

PSEUDOVIEWER2: visualization of RNA pseudoknots of any type
Nucl. Acids Res. 2003 31: 3432-3440; doi:10.1093/nar/gkg539 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Peter Bengert and Thomas Dandekar

A software tool-box for analysis of regulatory RNA elements
Nucl. Acids Res. 2003 31: 3441-3445; doi:10.1093/nar/gkg568 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Yuh-Jyh Hu

GPRM: a genetic programming approach to finding common RNA secondary structure elements
Nucl. Acids Res. 2003 31: 3446-3449; doi:10.1093/nar/gkg521 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3450-3460; doi:10.1093/nar/gkg529 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3461-3467; doi:10.1093/nar/gkg591 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3468-3470; doi:10.1093/nar/gkg615 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Steen Knudsen, Christopher Workman, Thomas Sicheritz-Ponten, and Carsten Friis

GenePublisher: automated analysis of DNA microarray data
Nucl. Acids Res. 2003 31: 3471-3476; doi:10.1093/nar/gkg629 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3477-3482; doi:10.1093/nar/gkg628 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Sheng Zhong, Cheng Li, and Wing Hung Wong

ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis
Nucl. Acids Res. 2003 31: 3483-3486; doi:10.1093/nar/gkg598 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3487-3490; doi:10.1093/nar/gkg630 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Henrik Bjørn Nielsen, Rasmus Wernersson, and Steen Knudsen

Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
Nucl. Acids Res. 2003 31: 3491-3496; doi:10.1093/nar/gkg622 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3497-3500; doi:10.1093/nar/gkg500 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3501-3502; doi:10.1093/nar/gkg502 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Olivier Poirot, Eamonn O'Toole, and Cedric Notredame

Tcoffee@igs: a web server for computing, evaluating and combining multiple sequence alignments
Nucl. Acids Res. 2003 31: 3503-3506; doi:10.1093/nar/gkg522 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Simon Cawley, Lior Pachter, and Marina Alexandersson

SLAM web server for comparative gene finding and alignment
Nucl. Acids Res. 2003 31: 3507-3509; doi:10.1093/nar/gkg583 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3510-3517; doi:10.1093/nar/gkg501 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3518-3524; doi:10.1093/nar/gkg579 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Nicolas Bray and Lior Pachter

MAVID multiple alignment server
Nucl. Acids Res. 2003 31: 3525-3526; doi:10.1093/nar/gkg623 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Liliana Florea, Michael McClelland, Cathy Riemer, Scott Schwartz, and Webb Miller

EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae
Nucl. Acids Res. 2003 31: 3527-3532; doi:10.1093/nar/gkg551 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3533-3536; doi:10.1093/nar/gkg561 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rasmus Wernersson and Anders Gorm Pedersen

RevTrans: multiple alignment of coding DNA from aligned amino acid sequences
Nucl. Acids Res. 2003 31: 3537-3539; doi:10.1093/nar/gkg609 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

V. Solovyev and I. Shahmuradov

PromH: promoters identification using orthologous genomic sequences
Nucl. Acids Res. 2003 31: 3540-3545; doi:10.1093/nar/gkg525 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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. 2003 31: 3546-3553; doi:10.1093/nar/gkg604 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Anason S. Halees, Dmitriy Leyfer, and Zhiping Weng

PromoSer: a large-scale mammalian promoter and transcription start site identification service
Nucl. Acids Res. 2003 31: 3554-3559; doi:10.1093/nar/gkg549 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Vladimir B. Bajic and Seng Hong Seah

Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes
Nucl. Acids Res. 2003 31: 3560-3563; doi:10.1093/nar/gkg570 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Anton Nekrutenko, Wen-Yu Chung, and Wen-Hsiung Li

ETOPE: evolutionary test of predicted exons
Nucl. Acids Res. 2003 31: 3564-3567; doi:10.1093/nar/gkg597 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3568-3571; doi:10.1093/nar/gkg616 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3572-3575; doi:10.1093/nar/gkg511 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3576-3579; doi:10.1093/nar/gkg585 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

William Thompson, Eric C. Rouchka, and Charles E. Lawrence

Gibbs Recursive Sampler: finding transcription factor binding sites
Nucl. Acids Res. 2003 31: 3580-3585; doi:10.1093/nar/gkg608 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Saurabh Sinha and Martin Tompa

YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
Nucl. Acids Res. 2003 31: 3586-3588; doi:10.1093/nar/gkg618 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3589-3592; doi:10.1093/nar/gkg544 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Jacques van Helden

Regulatory Sequence Analysis Tools
Nucl. Acids Res. 2003 31: 3593-3596; doi:10.1093/nar/gkg567 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Shannon D. Schlueter, Qunfeng Dong, and Volker Brendel

GeneSeqer@PlantGDB: gene structure prediction in plant genomes
Nucl. Acids Res. 2003 31: 3597-3600; doi:10.1093/nar/gkg533 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

William H. Majoros, Mihaela Pertea, Corina Antonescu, and Steven L. Salzberg

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders
Nucl. Acids Res. 2003 31: 3601-3604; doi:10.1093/nar/gkg527 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3605-3607; doi:10.1093/nar/gkg517 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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. 2003 31: 3608-3612; doi:10.1093/nar/gkg548 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3613-3617; doi:10.1093/nar/gkg602 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Giovanna Ambrosini, Viviane Praz, Vidhya Jagannathan, and Philipp Bucher

Signal search analysis server
Nucl. Acids Res. 2003 31: 3618-3620; doi:10.1093/nar/gkg611 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Pingping Guan, Irini A. Doytchinova, Christianna Zygouri, and Darren R. Flower

MHCPred: a server for quantitative prediction of peptide–MHC binding
Nucl. Acids Res. 2003 31: 3621-3624; doi:10.1093/nar/gkg510 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3625-3630; doi:10.1093/nar/gkg545 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3631-3634; doi:10.1093/nar/gkg537 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3635-3641; doi:10.1093/nar/gkg584 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Andrew Kernytsky and Burkhard Rost

Static benchmarking of membrane helix predictions
Nucl. Acids Res. 2003 31: 3642-3644; doi:10.1093/nar/gkg532 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3645-3650; doi:10.1093/nar/gkg621 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3651-3653; doi:10.1093/nar/gkg605 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Gitanjali Yadav, Rajesh S. Gokhale, and Debasisa Mohanty

SEARCHPKS: a program for detection and analysis of polyketide synthase domains
Nucl. Acids Res. 2003 31: 3654-3658; doi:10.1093/nar/gkg607 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Guojun Yang and Timothy C. Hall

MAK, a computational tool kit for automated MITE analysis
Nucl. Acids Res. 2003 31: 3659-3665; doi:10.1093/nar/gkg531 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Martin C. Frith, Michael C. Li, and Zhiping Weng

Cluster-Buster: finding dense clusters of motifs in DNA sequences
Nucl. Acids Res. 2003 31: 3666-3668; doi:10.1093/nar/gkg540 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

David Robelin, Hugues Richard, and Bernard Prum

SIC: a tool to detect short inverted segments in a biological sequence
Nucl. Acids Res. 2003 31: 3669-3671; doi:10.1093/nar/gkg596 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Roman Kolpakov, Ghizlane Bana, and Gregory Kucherov

mreps: efficient and flexible detection of tandem repeats in DNA
Nucl. Acids Res. 2003 31: 3672-3678; doi:10.1093/nar/gkg617 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

H. Richard and G. Nuel

SPA: simple web tool to assess statistical significance of DNA patterns
Nucl. Acids Res. 2003 31: 3679-3681; doi:10.1093/nar/gkg613 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Moshe Gal, Tzvi Katz, Amir Ovadia, and Gad Yagil

TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts
Nucl. Acids Res. 2003 31: 3682-3685; doi:10.1093/nar/gkg625 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Kristian Vlahovicek, László Kaján, and Sándor Pongor

DNA analysis servers: plot.it, bend.it, model.it and IS
Nucl. Acids Res. 2003 31: 3686-3687; doi:10.1093/nar/gkg559 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Tamas Vincze, Janos Posfai, and Richard J. Roberts

NEBcutter: a program to cleave DNA with restriction enzymes
Nucl. Acids Res. 2003 31: 3688-3691; doi:10.1093/nar/gkg526 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3692-3697; doi:10.1093/nar/gkg600 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Paul D. Taylor, Teresa K. Attwood, and Darren R. Flower

BPROMPT: a consensus server for membrane protein prediction
Nucl. Acids Res. 2003 31: 3698-3700; doi:10.1093/nar/gkg554 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Rune Linding, Robert B. Russell, Victor Neduva, and Toby J. Gibson

GlobPlot: exploring protein sequences for globularity and disorder
Nucl. Acids Res. 2003 31: 3701-3708; doi:10.1093/nar/gkg519 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Barbara Brannetti and Manuela Helmer-Citterich

iSPOT: a web tool to infer the interaction specificity of families of protein modules
Nucl. Acids Res. 2003 31: 3709-3711; doi:10.1093/nar/gkg592 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Steffen Hennig, Detlef Groth, and Hans Lehrach

Automated Gene Ontology annotation for anonymous sequence data
Nucl. Acids Res. 2003 31: 3712-3715; doi:10.1093/nar/gkg582 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3716-3719; doi:10.1093/nar/gkg566 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3720-3722; doi:10.1093/nar/gkg603 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Stéphanie Bocs, Stéphane Cruveiller, David Vallenet, Grégory Nuel, and Claudine Médigue

AMIGene: Annotation of MIcrobial Genes
Nucl. Acids Res. 2003 31: 3723-3726; doi:10.1093/nar/gkg590 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Hideaki Sugawara and Satoru Miyazaki

AHMII: Agent to Help Microbial Information Integration
Nucl. Acids Res. 2003 31: 3727-3728; doi:10.1093/nar/gkg523 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3729-3735; doi:10.1093/nar/gkg542 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Jason McDermott and Ram Samudrala

Bioverse: functional, structural and contextual annotation of proteins and proteomes
Nucl. Acids Res. 2003 31: 3736-3737; doi:10.1093/nar/gkg550 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3738-3741; doi:10.1093/nar/gkg610 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

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. 2003 31: 3742-3745; doi:10.1093/nar/gkg586 [Abstract] [FREE Full Text] [Print PDF] [Supplementary Material] [Request Permissions]  

Scott J. Emrich, Mary Lowe, and Arthur L. Delcher

PROBEmer: a web-based software tool for selecting optimal DNA oligos
Nucl. Acids Res. 2003 31: 3746-3750; doi:10.1093/nar/gkg569 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3751-3754; doi:10.1093/nar/gkg560 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Guoqing Lu, Michael Hallett, Stephanie Pollock, and David Thomas

DePIE: Designing Primers for Protein Interaction Experiments
Nucl. Acids Res. 2003 31: 3755-3757; doi:10.1093/nar/gkg577 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

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. 2003 31: 3758-3762; doi:10.1093/nar/gkg580 [Abstract] [FREE Full Text] [Print PDF] [Request Permissions]  

Timothy Rose, Jorja Henikoff, and Steven Henikoff

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design
Nucl. Acids Res. 2003 31: 3763-3766; doi:10.1093/nar/gkg524 [Abstract] [FREE Full Text] [Print PD