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Nucleic Acids Research, Volume 34
Volume 34, Database-Issue, January 1 2006
- Alex Bateman:
EDITORIAL. 1
- Michael Y. Galperin
:
The Molecular Biology Database Collection: 2006 update. 3-5 - Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori, Yoshio Tateno:
DDBJ in preparation for overview of research activities behind data submissions. 6-9 - Guy Cochrane
EMBL Nucleotide Sequence Database: developments in 2005. 10-15 - Dennis A. Benson, Ilene Karsch-Mizrachi
GenBank. 16-20 - Namshin Kim
ChimerDB - a knowledgebase for fusion sequences. 21-24 - K. T. Nishant, Chetan Kumar, M. R. S. Rao:
HUMHOT: a database of human meiotic recombination hot spots. 25-28 - Rivka L. Glaser, Joshua P. Ramsay
The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations. 29-31 - Patricia Siguier
ISfinder: the reference centre for bacterial insertion sequences. 32-36 - Grant H. Jacobs, Peter A. Stockwell, Warren Tate, Chris M. Brown:
Transterm - extended search facilities and improved integration with other databases. 37-40 - Jeremy D. Glasner, Michael Rusch, Paul Liss, Guy Plunkett III, Eric L. Cabot, Aaron E. Darling
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. 41-45 - Stefan Stamm, Jean-Jack M. Riethoven
ASD: a bioinformatics resource on alternative splicing. 46-55 - Dirk Holste, George Huo, Vivian Tung, Christopher B. Burge:
HOLLYWOOD: a comparative relational database of alternative splicing. 56-62 - Enrique Blanco
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters. 63-67 - Gordon Robertson, Misha Bilenky, Keven Lin, An He, W. Yuen, M. Dagpinar, Richard Varhol, Kevin Teague, Obi L. Griffith
cisRED: a database system for genome-scale computational discovery of regulatory elements. 68-73 - Sarah K. Kummerfeld
DBD: a transcription factor prediction database. 74-81 - Christoph D. Schmid, Rouaïda Périer, Viviane Praz, Philipp Bucher:
EPD in its twentieth year: towards complete promoter coverage of selected model organisms. 82-85 - Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano:
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. 86-89 - Vidhya Jagannathan, Emmanuelle Roulet, Mauro Delorenzi, Philipp Bucher:
HTPSELEX - a database of high-throughput SELEX libraries for transcription factor binding sites. 90-94 - Dominique Vlieghe, Albin Sandelin
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. 95-97 - Hao Sun
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. 98-103 - Xin Chen, Jianmin Wu
TiProD: the Tissue-specific Promoter Database. 104-107 - V. Matys, Olga V. Kel-Margoulis, Ellen Fricke, Ines Liebich, Sigrid Land, A. Barre-Dirrie, Ingmar Reuter, D. Chekmenev, Mathias Krull, Klaus Hornischer, Nico Voss, Philip Stegmaier, Birgit Lewicki-Potapov, H. Saxel, Alexander E. Kel, Edgar Wingender
TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes. 108-110 - Tala Bakheet, Bryan R. G. Williams
ARED 3.0: the large and diverse AU-rich transcriptome. 111-114 - Priyanka Shahi, Serguei Loukianiouk, Andreas Bohne-Lang
Argonaute - a database for gene regulation by mammalian microRNAs. 115-118 - Rumen Kostadinov
GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences. 119-124 - Martin Mokrejs
IRESite: the database of experimentally verified IRES structures (www.iresite.org). 125-130 - Liliana R. Stefan, Rui Zhang, Aaron G. Levitan, Donna K. Hendrix, Steven E. Brenner, Stephen R. Holbrook:
MeRNA: a database of metal ion binding sites in RNA structures. 131-134 - Paul Wei-Che Hsu, Hsien-Da Huang, Sheng-Da Hsu
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. 135-139 - Sam Griffiths-Jones
miRBase: microRNA sequences, targets and gene nomenclature. 140-144 - Stanislaw Dunin-Horkawicz
MODOMICS: a database of RNA modification pathways. 145-149 - Tao Wu
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. 150-152 - Andrew J. Olson, Nihar Sheth, Jason S. Lee, G. J. Hannon, Ravi Sachidanandam:
RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs. 153-157 - Laurent Lestrade, Michel J. Weber:
snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. 158-162 - Ebbe Sloth Andersen
The tmRDB and SRPDB resources. 163-168 - Hans-Werner Mewes, Dmitrij Frishman, Klaus F. X. Mayer, Martin Münsterkötter
MIPS: analysis and annotation of proteins from whole genomes in 2005. 169-172 - David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, David L. Kenton, Oleg Khovayko
Database resources of the National Center for Biotechnology Information. 173-180 - Milton H. Saier Jr., Can V. Tran, Ravi D. Barabote
TCDB: the Transporter Classification Database for membrane transport protein analyses and information. 181-186 - Cathy H. Wu
The Universal Protein Resource (UniProt): an expanding universe of protein information. 187-191 - Jason P. Mulvenna
CyBase: a database of cyclic protein sequence and structure. 192-194 - M. D. Shaji Kumar, M. Michael Gromiha:
PINT: Protein-protein Interactions Thermodynamic Database. 195-198 - Christopher P. Toseland
PPD v1.0 - an integrated, web-accessible database of experimentally determined protein pKa values. 199-203 - M. D. Shaji Kumar, K. Abdulla Bava, M. Michael Gromiha, Ponraj Prabakaran
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. 204-206 - Michelle K. M. Chow
The REFOLD database: a tool for the optimization of protein expression and refolding. 207-212 - J. Lynn Fink
LOCATE: a mouse protein subcellular localization database. 213-217 - Anthony Kar Lun Leung, Laura Trinkle-Mulcahy, Yun Wah Lam
NOPdb: Nucleolar Proteome Database. 218-220 - Rainer B. Lanz, Zeljko Jericevic, William J. Zuercher, Chris Watkins, David L. Steffen, Ronald Margolis, Neil J. McKenna
Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community. 221-226 - Nicolas Hulo, Amos Bairoch
The PROSITE database. 227-230 - Nicola D. Gold, Richard M. Jackson:
SitesBase: a database for structure-based protein-ligand binding site comparisons. 231-234 - Aaron Birkland, Golan Yona:
BIOZON: a hub of heterogeneous biological data. 235-242 - V. S. Gowri, Oruganty Krishnadev, C. S. Swamy, Narayanaswamy Srinivasan:
MulPSSM: a database of multiple position-specific scoring matrices of protein domain families. 243-246 - Robert D. Finn
Pfam: clans, web tools and services. 247-251 - Thomas Rattei
SIMAP: the similarity matrix of proteins. 252-256 - Ivica Letunic
SMART 5: domains in the context of genomes and networks. 257-260 - Alexander A. Zamyatnin, Alexander S. Borchikov, Michail G. Vladimirov, Olga L. Voronina:
The EROP-Moscow oligopeptide database. 261-266 - Marco Donizelli, Marie-Ange Djite, Nicolas Le Novère:
LGICdb: a manually curated sequence database after the genomes. 267-269 - Neil D. Rawlings
MEROPS: the peptidase database. 270-272 - Chittibabu Guda, Lipika R. Pal
DMAPS: a database of multiple alignments for protein structures. 273-276 - Zhanwen Li, Yuzhen Ye, Adam Godzik
Flexible Structural Neighborhood - a database of protein structural similarities and alignments. 277-280 - Corin Yeats, Michael Maibaum, Russell L. Marsden, Mark Dibley, David A. Lee, Sarah Addou, Christine A. Orengo:
Gene3D: modelling protein structure, function and evolution. 281-284 - Ganesan Pugalenthi, Anirban Bhaduri, Ramanathan Sowdhamini:
iMOTdb - a comprehensive collection of spatially interacting motifs in proteins. 285-286 - Mohammed Tagari, John G. Tate
E-MSD: improving data deposition and structure quality. 287-290 - Ursula Pieper
MODBASE: a database of annotated comparative protein structure models and associated resources. 291-295 - Samuel Flores
The Database of Macromolecular Motions: new features added at the decade mark. 296-301 - Andrei Kouranov, Lei Xie, Joanna de la Cruz, Li Chen, John D. Westbrook, Philip E. Bourne, Helen M. Berman
The RCSB PDB information portal for structural genomics. 302-305 - Tiziana Castrignanò, Paolo D'Onorio De Meo, Domenico Cozzetto
The PMDB Protein Model Database. 306-309 - Christof Winter
SCOPPI: a structural classification of protein-protein interfaces. 310-314 - Jürgen Kopp, Torsten Schwede
The SWISS-MODEL Repository: new features and functionalities. 315-318 - Tina A. Eyre, Fabrice Ducluzeau, Tam P. Sneddon, Sue Povey, Elspeth A. Bruford
The HUGO Gene Nomenclature Database, 2006 updates. 319-321 - The Gene Ontology (GO) project in 2006. 322-326
- Simon Whelan, Paul I. W. de Bakker, Emmanuel Quevillon, Nicolas Rodriguez
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. 327-331 - Konstantinos Liolios, Nektarios Tavernarakis
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. 332-334 - Roy R. Chaudhuri
xBASE, a collection of online databases for bacterial comparative genomics. 335-337 - Emmanuel Perrodou, Caroline Deshayes, Jean Muller
ICDS database: interrupted CoDing sequences in prokaryotic genomes. 338-343 - Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan
The integrated microbial genomes (IMG) system. 344-348 - Ingo Paulsen, Arndt von Haeseler:
INVHOGEN: a database of homologous invertebrate genes. 349-353 - Minoru Kanehisa, Susumu Goto, Masahiro Hattori, Kiyoko F. Aoki-Kinoshita
From genomics to chemical genomics: new developments in KEGG. 354-357 - Shujiro Okuda
ODB: a database of operons accumulating known operons across multiple genomes. 358-362 - Feng Chen, Aaron J. Mackey, Christian J. Stoeckert Jr., David S. Roos
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. 363-368 - Natalia Maltsev, Elizabeth M. Glass, Dinanath Sulakhe, Alexis A. Rodriguez, Mustafa H. Syed, Tanuja Bompada, Yi Zhang, Mark D'Souza:
PUMA2 - grid-based high-throughput analysis of genomes and metabolic pathways. 369-372 - Huiquan Wang, Miroslava Kaloper, Craig J. Benham:
SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes. 373-378 - Sucheta Tripathy
VMD: a community annotation database for oomycetes and microbial genomes. 379-381 - Michael J. Adams, John F. Antoniw:
DPVweb: a comprehensive database of plant and fungal virus genes and genomes. 382-385 - Craig M. Shepherd, Ian A. Borelli, Gabriel Lander, Padmaja Natarajan, Vinay Siddavanahalli, Chandrajit L. Bajaj, John E. Johnson, Charles L. Brooks III, Vijay S. Reddy:
VIPERdb: a relational database for structural virology. 386-389 - Thierry Lombardot
Megx.net - database resources for marine ecological genomics. 390-393 - Heladia Salgado, Socorro Gama-Castro, Martín Peralta-Gil, Edgar Díaz-Peredo, Fabiola Sánchez-Solano, Alberto Santos-Zavaleta, Irma Martínez-Flores
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. 394-397 - Jian Yang
ShiBASE: an integrated database for comparative genomics of Shigella. 398-401 - Guido Dieterich, Uwe Kärst, Elmar Fischer, Jürgen Wehland, Lothar Jänsch:
LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species. 402-406 - Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl, Todd M. Lowe:
The UCSC Archaeal Genome Browser. 407-410 - Gopa R. Mishra, M. Suresh, K. Kumaran, N. Kannabiran, Shubha Suresh, P. Bala, K. Shivakumar, N. Anuradha, Raghunath Reddy, T. Madhan Raghavan, Shalini Menon
Human protein reference database - 2006 update. 411-414 - Alexander Mehrle, Heiko Rosenfelder, Ingo Schupp, Coral del Val
The LIFEdb database in 2006. 415-418 - Mark Heiges, Haiming Wang, Edward Robinson, Cristina Aurrecoechea, Xin Gao, Nivedita Kaluskar, Philippa M. Rhodes, Sammy Wang, Congzhou He, Yanqi Su, John A. Miller
CryptoDB: a Cryptosporidium bioinformatics resource update. 419-422 - Rex L. Chisholm
dictyBase, the model organism database for Dictyostelium discoideum. 423-427 - Fernán Agüero, Wenlong Zheng, D. Brent Weatherly, Pablo N. Mendes
TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi. 428-431 - David James Sherman
Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. 432-435 - Ulrich Güldener
MPact: the MIPS protein interaction resource on yeast. 436-441 - Jodi E. Hirschman, Rama Balakrishnan, Karen R. Christie
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. 442-445 - Miguel C. Teixeira
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. 446-451 - Kevin P. Byrne
Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. 452-455 - Ulrich Güldener
FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum. 456-458 - Rainer Winnenburg, Thomas K. Baldwin, Martin Urban, Christopher J. Rawlings, Jacob Köhler, Kim E. Hammond-Kosack:
PHI-base: a new database for pathogen host interactions. 459-464 - Kamal Gajendran, Michael D. Gonzales, Andrew D. Farmer, Eric Archuleta, Joe Win, Mark E. Waugh, Sophien Kamoun:
Phytophthora functional genomics database (PFGD): functional genomics of phytophthora-plant interactions. 465-470 - David H. Johnson, Jun Tsao, Ming Luo, Mike Carson:
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans. 471-474 - Erich M. Schwarz
WormBase: better software, richer content. 475-478 - David Sims
FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets. 479-483 - Gary Grumbling, Victor B. Strelets:
FlyBase: anatomical data, images and queries. 484-488 - Ian Flockhart, Matthew Booker, Amy Kiger, Michael Boutros
FlyRNAi: the Drosophila RNAi screening center database. 489-494 - James C. Sullivan, Joseph F. Ryan
StellaBase: The Nematostella vectensis Genomics Database. 495-499 - Nicholas A. Stover, Cynthia J. Krieger, Gail Binkley, Qing Dong, Dianna G. Fisk, Robert S. Nash, Anand Sethuraman, Shuai Weng, J. Michael Cherry
Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. 500-503 - Gary D. Bader
Pathguide: a Pathway Resource List. 504-506 - Dawn Cotter, Andreia Maer, Chittibabu Guda, Brian Saunders, Shankar Subramaniam:
LMPD: LIPID MAPS proteome database. 507-510 - Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne M. Paley, John Pick, Seung Yon Rhee, Christophe Tissier, Peifen Zhang, Peter D. Karp
MetaCyc: a multiorganism database of metabolic pathways and enzymes. 511-516 - Lynda B. M. Ellis, Dave Roe, Lawrence P. Wackett:
The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. 517-521 - Peter Block, Christoph A. Sotriffer, Ingo Dramburg, Gerhard Klebe:
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB. 522-526 - Aylwin Ng, Borisas Bursteinas
pSTIING: a "systems" approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. 527-534 - Chris Stark, Bobby-Joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Mike Tyers:
BioGRID: a general repository for interaction datasets. 535-539 - Anatolij Potapov, Ines Liebich, Jürgen Dönitz, Knut Schwarzer, Nicole Sasse, Torsten Schoeps, Torsten Crass, Edgar Wingender
EndoNet: an information resource about endocrine networks. 540-545 - Mathias Krull, Susanne Pistor, Nico Voss, Alexander E. Kel, Ingmar Reuter, Deborah Kronenberg
TRANSPATH®: an information resource for storing and visualizing signaling pathways and their pathological aberrations. 546-551 - Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai:
DBTGR: a database of tunicate promoters and their regulatory elements. 552-555 - Ewan Birney
Ensembl 2006. 556-561 - Judith A. Blake, Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database (MGD): updates and enhancements. 562-567 - Andreas Ruepp, Octave Noubibou Doudieu, Jos van den Oever, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, Christine Skornia, Steffi Wanka, Thomas Rattei
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. 568-571 - Heng Li
TreeFam: a curated database of phylogenetic trees of animal gene families. 572-580 - Judy Sprague, Leyla Bayraktaroglu, Dave Clements
The Zebrafish Information Network: the zebrafish model organism database. 581-585 - Kremena V. Star, Quingbin Song, Andy Zhu, Erwin P. Böttinger:
QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL. 586-589 - Angela S. Hinrichs, Donna Karolchik, Robert Baertsch, Galt P. Barber, Gill Bejerano, Hiram Clawson
The UCSC Genome Browser Database: update 2006. 590-598 - Johann Lenffer, Frank W. Nicholas
OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI. 599-601 - Ghazi O. Tadmouri
CTGA: the database for genetic disorders in Arab populations. 602-606 - Xiaosong Wang, Haitao Zhao, Qingwen Xu, Weibo Jin, Changning Liu, Huagang Zhang, Zhibin Huang, Xinyu Zhang, Yu Zhang, Dianqi Xin, Andrew J. G. Simpson, Lloyd J. Old, Yanqun Na, Yi Zhao, Weifeng Chen:
HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. 607-612 - Adil Elfilali, Séverine Lair, Catia Verbeke, Philippe La Rosa, François Radvanyi, Emmanuel Barillot
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. 613-616 - Bernice R. Packer, Meredith Yeager, Laura Burdett, Robert Welch, Michael Beerman, Liqun Qi, Hugues Sicotte, Brian Staats
SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. 617-621 - Tzong-Yi Lee, Hsien-Da Huang, Jui-Hung Hung
dbPTM: an information repository of protein post-translational modification. 622-627 - Osamu Ogasawara
BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. 628-631 - Hideya Kawaji
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. 632-636 - Jeffrey H. Christiansen, Yiya Yang, Shanmugasundaram Venkataraman
EMAGE: a spatial database of gene expression patterns during mouse embryo development. 637-641 - Alex S. Nord
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. 642-648 - Thomas McLaughlin, Jennifer A. Siepen, Julian N. Selley
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns. 649-654 - Frank Desiere, Eric W. Deutsch, Nichole L. King, Alexey I. Nesvizhskii
The PeptideAtlas project. 655-658 - Philip Jones, Richard G. Côté, Lennart Martens
PRIDE: a public repository of protein and peptide identifications for the proteomics community. 659-663 - Xiaochen Bo
AOBase: a database for antisense oligonucleotides selection and design. 664-667 - David S. Wishart, Craig Knox, Anchi Guo, Savita Shrivastava, Murtaza Hassanali, Paul Stothard, Zhan Chang, Jennifer Woolsey:
DrugBank: a comprehensive resource for in silico drug discovery and exploration. 668-672 - Yasushi Okuno, Jiyoon Yang, Kei Taneishi, Hiroaki Yabuuchi
GLIDA: GPCR-ligand database for chemical genomic drug discovery. 673-677 - Mathias Dunkel
SuperNatural: a searchable database of available natural compounds. 678-683 - Filip Pattyn
RTPrimerDB: the real-time PCR primer and probe database, major update 2006. 684-688 - Nicolas Le Novère, Benjamin J. Bornstein, Alexander Broicher, Mélanie Courtot
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. 689-691 - Liying Cui, Narayanan Veeraraghavan, Alexander Richter, P. Kerr Wall, Robert K. Jansen, James H. Leebens-Mack
ChloroplastDB: the Chloroplast Genome Database. 692-696 - Emmet A. O'Brien, Yue Zhang, LiuSong Yang, Eric Wang, Veronique Marie, B. Franz Lang, Gertraud Burger:
GOBASE - a database of organelle and bacterial genome information. 697-699 - Jochen Kohl, Ingo Paulsen, Thomas Laubach, Achim Radtke, Arndt von Haeseler:
HvrBase++: a phylogenetic database for primate species. 700-704 - Holger Prokisch
MitoP2: the mitochondrial proteome database - now including mouse data. 705-711 - Davina K. Button, Kevan M. A. Gartland, Leslie D. Ball, Louis Natanson, Jill S. Gartland, Gary D. Lyon:
DRASTIC - INSIGHTS: querying information in a plant gene expression database. 712-716 - Pankaj Jaiswal, Junjian Ni, Immanuel Yap, Doreen Ware, William Spooner, Ken Youens-Clark, Liya Ren, Chengzhi Liang, Wei Zhao, Kiran Ratnapu, Benjamin Faga, Payan Canaran, Molly Fogleman, Claire Hebbard
Gramene: a bird's eye view of cereal genomes. 717-723 - Stefanie Hartmann, Dihui Lu, Jason Phillips, Todd J. Vision
Phytome: a platform for plant comparative genomics. 724-730 - Mayumi Nakano
Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. 731-735 - Gaëtan Droc
OryGenesDB: a database for rice reverse genetics. 736-740 - Hajime Ohyanagi, Tsuyoshi Tanaka
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. 741-744 - Jianwei Zhang
RMD: a rice mutant database for functional analysis of the rice genome. 745-748 - Max Ingman, Ulf Gyllensten:
mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. 749-751 - Wei Zhao, Payan Canaran, Rebecca Jurkuta, Theresa Fulton, Jeffrey Glaubitz, Edward S. Buckler
Panzea: a database and resource for molecular and functional diversity in the maize genome. 752-757 - Jeffry L. Shultz, Deepak Kurunam, Kay Shopinski, M. Javed Iqbal, Samreen Kazi, Kimberley Zobrist, Rabia Bashir, Satsuki Yaegashi, Nagajyothi Lavu, Ahmed J. Afzal, Charles R. Yesudas, M. Abdelmajid Kassem, Chengcang Wu, Hong Bin Zhang, Christopher D. Town, Khalid Meksem
The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. 758-765 - Zhangjun Fei, Xuemei Tang, Rob Alba, James J. Giovannoni:
Tomato Expression Database (TED): a suite of data presentation and analysis tools. 766-770 - Agnes P. Chan
The TIGR Maize Database. 771-776 - Avner Schlessinger, Yanay Ofran, Guy Yachdav, Burkhard Rost
Epitome: database of structure-inferred antigenic epitopes. 777-780 - Véronique Giudicelli
IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. 781-784
Volume 34, Number Web-Server-Issue, 1 July 2006
- Editorial. 1
- Joanne A. Fox, Scott McMillan, B. F. Francis Ouellette
A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory. 3-5 - Jian Ye, Scott D. McGinnis, Thomas L. Madden:
BLAST: improvements for better sequence analysis. 6-9 - Jeanette Tångrot, Lixiao Wang, Bo Kågström, Uwe H. Sauer:
FISH - family identification of sequence homologues using structure anchored hidden Markov models. 10-14 - Markus Rampp, Thomas Soddemann, Hermann Lederer:
The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. 15-19 - Yuko Tsuchiya, Kengo Kinoshita, Nobutoshi Ito, Haruki Nakamura:
PreBI: prediction of biological interfaces of proteins in crystals. 20-24 - Hanjo Täubig, Arno Buchner
PAST: fast structure-based searching in the PDB. 20-23 - Lee-Wei Yang, A. J. Rader, Xiong Liu
oGNM: online computation of structural dynamics using the Gaussian Network Model. 24-31 - Ze-Rong Li, Honghuang Lin
PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. 32-37 - Cyril Azuara, Erik Lindahl
PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. 38-42 - Alexander A. Kantardjiev, Boris P. Atanasov:
PHEPS: web-based pH-dependent Protein Electrostatics Server. 43-47 - Barbara M. Tynan-Connolly, Jens Erik Nielsen
pKD: re-designing protein pKa values. 48-51 - Erik Lindahl
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. 52-56 - Yunho Jang, Jay il Jeong
UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models. 57-62 - Mark V. Berjanskii, Stephen Neal, David S. Wishart
PREDITOR: a web server for predicting protein torsion angle restraints. 63-69 - M. Michael Gromiha, A. Mary Thangakani, Samuel Selvaraj:
FOLD-RATE: prediction of protein folding rates from amino acid sequence. 70-74 - Jean-Christophe Gelly
Protein Peeling 2: a web server to convert protein structures into series of protein units. 75-78 - Razif R. Gabdoulline
ProSAT2 - Protein Structure Annotation Server. 79-83 - Rasmus Wernersson
FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB. 84-88 - Jui-Hung Hung
ProKware: integrated software for presenting protein structural properties in protein tertiary structures. 89-94 - Edward S. C. Shih, Ruei-chi R. Gan, Ming-Jing Hwang:
OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures. 95-98 - Sunghoon Lee
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. 99-103 - Blaise T. F. Alako
TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure. 104-109 - Angel Carro, Michael L. Tress
TreeDet: a web server to explore sequence space. 110-115 - Joe Dundas, Zheng Ouyang, Jeffery Tseng, T. Andrew Binkowski, Yaron Turpaz, Jie Liang:
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. 116-118 - Manoj Tyagi, P. Sharma, C. S. Swamy, F. Cadet, Narayanaswamy Srinivasan, Alexandre G. de Brevern
Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. 119-123 - Shandar Ahmad
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. 124-127 - K. Sumathi, P. Ananthalakshmi, M. N. A. Mohd. Roshan, Krishna Sekar:
3dSS: 3D structural superposition. 128-132 - Hatice Gulcin Ozer, William C. Ray
MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments. 133-136 - Johannes Söding
HHrep: de novo protein repeat detection and the origin of TIM barrels. 137-142 - Rana Bhadra, Sankaran Sandhya
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. 143-146 - Julien Maupetit
SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. 147-151 - Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang
(PS)2: protein structure prediction server. 152-157 - Lusheng Chen, Wei Wang
KemaDom: a web server for domain prediction using kernel machine with local context. 158-163 - Alessandro Vullo
Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines. 164-168 - Mauro Amico, Michele Finelli, Ivan Rossi
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. 169-172 - Narcis Fernandez-Fuentes
ArchPRED: a template based loop structure prediction server. 173-176 - Alessio Ceroni, Andrea Passerini
DISULFIND: a disulfide bonding state and cysteine connectivity prediction server. 177-181 - Fabrizio Ferrè
DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification. 182-185 - Henry R. Bigelow, Burkhard Rost
PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. 186-188 - Jérôme Waldispühl, Bonnie Berger, Peter Clote, Jean-Marc Steyaert:
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. 189-193 - Pierre Dönnes
SVMHC: a server for prediction of MHC-binding peptides. 194-197 - Tun-Wen Pai, Margaret Dah-Tsyr Chang, Wen-Shyong Tzou, Bo-Han Su, Pei-Chih Wu, Hao-Teng Chang, Wei-I Chou:
REMUS: a tool for identification of unique peptide segments as epitopes. 198-201 - Sudipto Saha
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. 202-209 - Chittibabu Guda:
pTARGET: a web server for predicting protein subcellular localization. 210-213 - Maria Novatchkova, Georg Schneider, Richard Fritz, Frank Eisenhaber
DOUTfinder - identification of distant domain outliers using subsignificant sequence similarity. 214-218 - Honglin Li, Zhenting Gao, Ling Kang, Hailei Zhang, Kun Yang, Kunqian Yu, Xiaomin Luo
TarFisDock: a web server for identifying drug targets with docking approach. 219-224 - Ana P. C. Rodrigues
sgTarget: a target selection resource for structural genomics. 225-230 - Ganesan Pugalenthi
HARMONY: a server for the assessment of protein structures. 231-234 - Yi Liu, Brian Kuhlman:
RosettaDesign server for protein design. 235-238 - Vijaya Parthiban, M. Michael Gromiha, Dietmar Schomburg
CUPSAT: prediction of protein stability upon point mutations. 239-242 - Liangjiang Wang, Susan J. Brown
BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. 243-248 - Hu Chen, Yu Xue
MeMo: a web tool for prediction of protein methylation modifications. 249-253 - Yu Xue
SUMOsp: a web server for sumoylation site prediction. 254-257 - Sangtae Kim, Seungjin Na
MODi : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra. 258-263 - Nagarajan Harish, Rekha Gupta, Parul Agarwal, Vinod Scaria
DyNAVacS: an integrative tool for optimized DNA vaccine design. 264-266 - Bruce R. Southey
NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides. 267-272 - Anne de Jong, Sacha A. F. T. van Hijum, Jetta J. E. Bijlsma, Jan Kok, Oscar P. Kuipers
BAGEL: a web-based bacteriocin genome mining tool. 273-279 - Shu Ju Hsieh, Chun-Yuan Lin, Ning Han Liu, Wei Yuan Chow, Chuan Yi Tang:
GeneAlign: a coding exon prediction tool based on phylogenetical comparisons. 280-284 - Simona Rossi, Daniele Masotti, Christine Nardini
TOM: a web-based integrated approach for identification of candidate disease genes. 285-292 - Jia Ye, Lin Fang, Hongkun Zheng, Yong Zhang, Jie Chen, Zengjin Zhang, Jing Wang, Shengting Li, Ruiqiang Li, Lars Bolund, Jun Wang:
WEGO: a web tool for plotting GO annotations. 293-297 - Carlos Prieto
APID: Agile Protein Interaction DataAnalyzer. 298-302 - Darby Tien-Hao Chang, Yi-Zhong Weng, Jung-Hsin Lin
Protemot: prediction of protein binding sites with automatically extracted geometrical templates. 303-309 - Andrey Tovchigrechko, Ilya A. Vakser:
GRAMM-X public web server for protein-protein docking. 310-314 - José M. G. Izarzugaza, David de Juan
TSEMA: interactive prediction of protein pairings between interacting families. 315-319 - Laetitia Martin, Vincent Catherinot, Gilles Labesse
kinDOCK: a tool for comparative docking of protein kinase ligands. 325-329 - Christopher J. Penkett, James A. Morris, Valerie Wood
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms. 330-334 - Andreas Biegert, Christian E. Mayer, Michael Remmert, Johannes Söding
The MPI Bioinformatics Toolkit for protein sequence analysis. 335-339 - Naveed Massjouni, Corban G. Rivera, T. M. Murali:
VIRGO: computational prediction of gene functions. 340-344 - Chisato Yamasaki, Hiroaki Kawashima, Fusano Todokoro, Yasuhiro Imamizu, Makoto Ogawa
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB. 345-349 - Victor Neduva, Robert B. Russell
DILIMOT: discovery of linear motifs in proteins. 350-355 - Chen-Ming Hsu, Chien-Yu Chen
MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences. 356-361 - Edouard De Castro
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. 362-365 - Shane J. Neph, Martin Tompa:
MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. 366-368 - Timothy L. Bailey, Nadya Williams, Chris Misleh, Wilfred W. Li:
MEME: discovering and analyzing DNA and protein sequence motifs. 369-373 - Johannes Söding
HHsenser: exhaustive transitive profile search using HMM-HMM comparison. 374-378 - Iddo Friedberg
JAFA: a protein function annotation meta-server. 379-381 - Han Liang
SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis. 382-384 - Rasmus Wernersson
Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation. 385-388 - Federico Abascal, Rafael Zardoya
GenDecoder: genetic code prediction for metazoan mitochondria. 389-393 - Todd Z. DeSantis, Philip Hugenholtz
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. 394-399 - Tobias Dezulian, Martin H. Schaefer
CrossLink: visualization and exploration of sequence relationships between (micro) RNAs. 400-404 - Eckart Bindewald, Thomas D. Schneider
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments. 405-411 - Oranit Dror, Ruth Nussinov
The ARTS web server for aligning RNA tertiary structures. 412-415 - Yanga Byun, Kyungsook Han:
PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. 416-422 - Tzu-Hao Chang
RNAMST: efficient and flexible approach for identifying RNA structural homologs. 423-428 - Hsi-Yuan Huang, Chia-Hung Chien, Kuan-Hua Jen, Hsien-Da Huang:
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. 429-434 - Mario Stanke, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, Burkhard Morgenstern:
AUGUSTUS: ab initio prediction of alternative transcripts. 435-439 - Tiziana Castrignanò, Raffaella Rizzi
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization. 440-443 - Durgaprasad Bollina, Bernett T. K. Lee, Tin Wee Tan, Shoba Ranganathan
ASGS: an alternative splicing graph web service. 444-447 - Yuki Naito
siVirus: web-based antiviral siRNA design software for highly divergent viral sequences. 448-450 - Jan Krüger, Marc Rehmsmeier:
RNAhybrid: microRNA target prediction easy, fast and flexible. 451-454 - Jin-Wu Nam, Jinhan Kim, Sung-Kyu Kim, Byoung-Tak Zhang:
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs. 455-458 - Ali Masoudi-Nejad
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. 459-462 - Ming Zhang, Anne-Kathrin Schultz
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. 463-465 - Michael Baitaluk, Mayya Sedova
BiologicalNetworks: visualization and analysis tool for systems biology. 466-471 - Fátima Al-Shahrour, Pablo Minguez
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. 472-476 - Stéphane Liva, Philippe Hupé
CAPweb: a bioinformatics CGH array Analysis Platform. 477-481 - Fabrizio Ferrè
BTW: a web server for Boltzmann time warping of gene expression time series. 482-485 - David Montaner
Next station in microarray data analysis: GEPAS. 486-491 - Yupeng Wang
GEPS: the Gene Expression Pattern Scanner. 492-497 - Johannes Rainer
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. 498-503 - Iain W. Manfield
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. 504-509 - Maurice Scheer, Frank Klawonn
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. 510-515 - Jeffrey G. Mandell, Carlos F. Barbas III:
Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. 516-523 - Ian John Donaldson, Berthold Göttgens
TFBScluster web server for the identification of mammalian composite regulatory elements. 524-528 - Jan Grau, Irad E. Ben-Gal, Stefan Posch, Ivo Grosse:
VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees. 529-533 - Matti Kankainen
POXO: a web-enabled tool series to discover transcription factor binding sites. 534-540 - T. Waleev, Dmitry Shtokalo
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm. 541-545 - Thomas Fiedler, Marc Rehmsmeier:
jPREdictor: a versatile tool for the prediction of cis-regulatory elements. 546-550 - Xuwo Ji, Wei Li, Jun Song
CEAS: cis-regulatory element annotation system. 551-554 - Saurabh Sinha, Yupu Liang, Eric D. Siggia:
Stubb: a program for discovery and analysis of cis-regulatory modules. 555-559 - Peter Luykx, Ivan V. Bajic
NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors. 560-565 - Giulio Pavesi
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes. 566-570 - Chun-Chi Liu, Chin-Chung Lin, Wen-Shyen E. Chen, Hsuan-Yu Chen, Pei-Chun Chang, Jeremy J. W. Chen
CRSD: a comprehensive web server for composite regulatory signature discovery. 571-577 - Aurélie Lardenois, Frédéric Chalmel
PromAn: an integrated knowledge-based web server dedicated to promoter analysis. 578-583 - Sarita Ranjan, Jayashree Seshadri, Vaibhav Vindal, Sailu Yellaboina, Akash Ranjan:
iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species. 584-587 - Maike Tech, Burkhard Morgenstern, Peter Meinicke:
TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites. 588-590 - Igor V. Deyneko, Björn Bredohl, Daniel Wesely, Yulia M. Kalybaeva, Alexander E. Kel, Helmut Blöcker, Gerhard Kauer:
FeatureScan: revealing property-dependent similarity of nucleotide sequences. 591-595 - Timo Lassmann
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. 596-599 - Sébastien Moretti
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. 600-603 - Fabrice Armougom, Sébastien Moretti
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. 604-608 - Mikita Suyama
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. 609-612 - Neil Christopher Jones, Degui Zhi, Benjamin J. Raphael:
AliWABA: alignment on the web through an A-Bruijn approach. 613-616 - Fei Fang, Mathieu Blanchette:
FootPrinter3: phylogenetic footprinting in partially alignable sequences. 617-620 - Lucía Conde
PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. 621-625 - Purvesh Khatri
New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. 626-631 - Sònia Casillas
PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA. 632-634 - Hsiang-Yu Yuan
FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. 635-641 - Areum Han, Hyo Jin Kang, Yoobok Cho, Sunghoon Lee, Young Joo Kim, Sungsam Gong
SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences. 642-644 - Paul D. Thomas
Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. 645-650 - Reidar Andreson
SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. 651-655 - Erica G. Jewell, Andrew Robinson
SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery. 656-659 - Fengxia Yao, Ruifang Zhang, Zanhua Zhu, Kun Xia, Chunyu Liu:
MutScreener: primer design tool for PCR-direct sequencing. 660-664 - Tomoyuki Yamada, Haruhiko Soma, Shinichi Morishita
PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome. 665-669 - Jakob Fredslund, Lene H. Madsen, Birgit K. Hougaard, Niels Sandal, Jens Stougaard
GeMprospector - online design of cross-species genetic marker candidates in legumes and grasses. 670-675 - Oleg Kikin, Lawrence D'Antonio
QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. 676-682 - Vinod Scaria
Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences. 683-685 - Feng Gao
GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. 686-691 - Philipp W. Messer
CorGen - measuring and generating long-range correlations for DNA sequence analysis. 692-695 - Ying Chih Lin, Chin Lung Lu, Ying-Chuan Liu, Chuan Yi Tang:
SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges. 696-699 - David Posada
ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online. 700-703 - Jörg Schultz, Tobias Müller, Marco Achtziger, Philipp N. Seibel, Thomas Dandekar
The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses. 704-707 - Gábor Tóth
PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats. 708-713 - Luca Pireddu
The Path-A metabolic pathway prediction web server. 714-719 - Jianmin Wu
KOBAS server: a web-based platform for automated annotation and pathway identification. 720-724 - Christopher Hyland
metaSHARK: a WWW platform for interactive exploration of metabolic networks. 725-728 - Duncan Hull
Taverna: a tool for building and running workflows of services. 729-732 - Alexander Loß, Roland Stenutz, Eberhard Schwarzer, Claus-Wilhelm von der Lieth:
GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface. 733-737 - Maria A. Miteva
FAF-Drugs: free ADME/tox filtering of compound collections. 738-744 - Alfred D. Eaton
HubMed: a web-based biomedical literature search interface. 745-747 - Uma Mudunuri, Robert M. Stephens, David Bruining, David Liu, Frank J. Lebeda:
botXminer: mining biomedical literature with a new web-based application. 748-752
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