| | Articles 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 |