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Nucleic Acids Research, Volume 35
Volume 35, Number Database-Issue, January 2007
- Alex Bateman:
Editorial. 1-2
- Michael Y. Galperin
:
The Molecular Biology Database Collection: 2007 update. 3-4 - David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar
Database resources of the National Center for Biotechnology Information. 5-12 - Hideaki Sugawara, Takashi Abe, Takashi Gojobori, Yoshio Tateno:
DDBJ working on evaluation and classification of bacterial genes in INSDC. 13-15 - Tamara Kulikova, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Lawrence Bower, Paul Browne, Matias Castro, Guy Cochrane
EMBL Nucleotide Sequence Database in 2006. 16-20 - Dennis A. Benson, Ilene Karsch-Mizrachi
GenBank. 21-25 - Donna R. Maglott, James Ostell, Kim D. Pruitt
Entrez Gene: gene-centered information at NCBI. 26-31 - Christoph Dieterich, M. W. Franz, Martin Vingron:
Developments in CORG: a gene-centric comparative genomics resource. 32-35 - Sunil Archak
InSatDb: a microsatellite database of fully sequenced insect genomes. 36-39 - Conrad A. Nieduszynski
OriDB: a DNA replication origin database. 40-46 - Byungwook Lee, Taehyung Kim, Seon-Kyu Kim
Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications. 47-50 - Lei Bao, Mi Zhou, Ligang Wu, Lu Lu, Dan Goldowitz
PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. 51-54 - John E. Karro, Yangpan Yan, Deyou Zheng
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. 55-60 - Kim D. Pruitt
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. 61-65 - Cristian Chaparro, Romain Guyot
RetrOryza: a database of the rice LTR-retrotransposons. 66-70 - Ino Agrafioti
SNPSTR: a database of compound microsatellite-SNP markers. 71-75 - Gang Wu
SGDB: a database of synthetic genes re-designed for optimizing protein over-expression. 76-79 - Yevgeniy Gelfand, Alfredo Rodriguez, Gary Benson:
TRDB - The Tandem Repeats Database. 80-87 - Axel Visel
VISTA Enhancer Browser - a database of tissue-specific human enhancers. 88-92 - Namshin Kim
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. 93-98 - Yeunsook Lee, Younghee Lee, Bumjin Kim, Youngah Shin, Seungyoon Nam
ECgene: an alternative splicing database update. 99-103 - Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi
H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. 104-109 - Tyler S. Alioto
U12DB: a database of orthologous U12-type spliceosomal introns. 110-115 - Anil G. Jegga
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs. 116-121 - Vincent Ferretti, Christian Poitras
PReMod: a database of genome-wide mammalian cis-regulatory module predictions. 122-126 - Mikhail Pachkov, Ionas Erb
SwissRegulon: a database of genome-wide annotations of regulatory sites. 127-131 - Abel González Pérez
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes. 132-136 - C. Jiang, Zhenyu Xuan, Fang Zhao, Michael Q. Zhang:
TRED: a transcriptional regulatory element database, new entries and other development. 137-140 - Tao He, Pufeng Du, Yanda Li:
dbRES: a web-oriented database for annotated RNA editing sites. 141-144 - Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, Kiyoshi Asai:
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. 145-148 - Molly Megraw
miRGen: a database for the study of animal microRNA genomic organization and function. 149-155 - Yong Zhang, Jiongtang Li, Lei Kong, Ge Gao, Qing-Rong Liu
NATsDB: Natural Antisense Transcripts DataBase. 156-161 - Maciej Szymanski
Noncoding RNAs database (ncRNAdb). 162-164 - Ju Youn Lee, Ijen Yeh, Ji Yeon Park, Bin Tian
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. 165-168 - James R. Cole, Benli Chai, Ryan J. Farris, Qiong Wang, A. S. Kulam-Syed-Mohideen, Donna M. McGarrell, A. M. Bandela, E. Cardenas, George M. Garrity
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. 169-172 - Ernesto Picardi
REDIdb: the RNA editing database. 173-177 - Ken C. Pang
RNAdb 2.0 - an expanded database of mammalian non-coding RNAs. 178-182 - Jun Xie, Ming Zhang, Tao Zhou, Xia Hua, LiSha Tang, Weilin Wu:
Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs. 183-187 - Michael Hiller, Swetlana Nikolajewa, Klaus Huse
TassDB: a database of alternative tandem splice sites. 188-192 - The Universal Protein Resource (UniProt). 193-197
- Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. 198-201 - Di Wu, Feng Cui, Robert L. Jernigan
PIDD: database for Protein Inter-atomic Distance Distributions. 202-207 - Andrea Pierleoni
eSLDB: eukaryotic subcellular localization database. 208-212 - Joshua L. Heazlewood
SUBA: the Arabidopsis Subcellular Database. 213-218 - Gonzalo López
FireDB - a database of functionally important residues from proteins of known structure. 219-223 - Nicola J. Mulder
New developments in the InterPro database. 224-228 - Andreas Zanzoni
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. 229-231 - Paolo Sonego
A Protein Classification Benchmark collection for machine learning. 232-236 - Aron Marchler-Bauer
CDD: a conserved domain database for interactive domain family analysis. 237-240 - Elon Portugaly, Nathan Linial, Michal Linial
EVEREST: a collection of evolutionary conserved protein domains. 241-246 - Huaiyu Mi, Nan Guo, Anish Kejariwal, Paul D. Thomas
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. 247-252 - Antonina Andreeva
SISYPHUS - structural alignments for proteins with non-trivial relationships. 253-259 - Jeremy D. Selengut, Daniel H. Haft
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. 260-264 - Shalin Seebah, Anita Suresh
Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. 265-268 - Richard J. Roberts
REBASE - enzymes and genes for DNA restriction and modification. 269-270 - Mark D'Souza, Elizabeth M. Glass, Mustafa H. Syed, Yi Zhang, Alexis A. Rodriguez, Natalia Maltsev, Michael Y. Galperin
Sentra: a database of signal transduction proteins for comparative genome analysis. 271-273 - Qinghu Ren, Kaixi Chen, Ian T. Paulsen
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. 274-279 - Philip V. Toukach
Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de. 280-286 - Martin Frank
GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages. 287-290 - Lesley H. Greene, Tony E. Lewis, Sarah Addou, Alison L. Cuff, Timothy Dallman, Mark Dibley, Oliver Redfern
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. 291-297 - Yanli Wang, Kenneth J. Addess, Jie Chen, Lewis Y. Geer
MMDB: annotating protein sequences with Entrez's 3D-structure database. 298-300 - Helen M. Berman
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. 301-303 - Kate F. Fulton, Mark A. Bate, Noel G. Faux
Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium. 304-307 - Derek Wilson, Martin Madera, Christine Vogel, Cyrus Chothia, Julian Gough:
The SUPERFAMILY database in 2007: families and functions. 308-313 - M. Michael Gromiha, Yukimitsu Yabuki, Srinesh Kundu, Sivasundaram Suharnan, Makiko Suwa
TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences. 314-316 - Chesley M. Leslin, Alexej Abyzov
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. 317-321 - Gil Alterovitz, Michael Xiang
GO PaD: the Gene Ontology Partition Database. 322-327 - Yuying Tian, Allan W. Dickerman:
GeneTrees: a phylogenomics resource for prokaryotes. 328-331 - T. Ryan Gregory, James A. Nicol, Heidi Tamm, Bellis Kullman, Kaur Kullman
Eukaryotic genome size databases. 332-338 - Masaki Hirahata, Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, Hideaki Sugawara:
Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes. 339-342 - Ikuo Uchiyama
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. 343-346 - Leslie Klis McNeil, Claudia Reich, Ramy K. Aziz
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. 347-353 - M. Louise Riley, Thorsten Schmidt
PEDANT genome database: 10 years online. 354-357 - Christian von Mering
STRING 7 - recent developments in the integration and prediction of protein interactions. 358-362 - Christophe Combet
euHCVdb: the European hepatitis C virus database. 363-366 - Saravanamuttu Gnaneshan
HepSEQ: International Public Health Repository for Hepatitis B. 367-370 - Calvin Pan, Joseph Kim, Lamei Chen, Qi Wang
The HIV positive selection mutation database. 371-375 - Suhua Chang, Jiajie Zhang, Xiaoyun Liao, Xinxing Zhu, Dahai Wang, Jiang Zhu, Tao Feng, Baoli Zhu, George F. Gao, Jian Wang, Huanming Yang
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. 376-380 - Paul Wei-Che Hsu, Li-Zen Lin, Sheng-Da Hsu
ViTa: prediction of host microRNAs targets on viruses. 381-385 - Luke E. Ulrich, Igor B. Zhulin
MiST: a microbial signal transduction database. 386-390 - Carol L. Ecale Zhou, Jason Smith, Marisa Lam, Adam T. Zemla, Matthew D. Dyer, Tom Slezak:
MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications. 391-394 - Sung Ho Yoon
Towards pathogenomics: a web-based resource for pathogenicity islands. 395-400 - E. E. Snyder, N. Kampanya, J. Lu, Eric K. Nordberg, H. R. Karur, Maulik Shukla, Jeetendra Soneja, Y. Tian, Tian Xue, Hyun Seung Yoo, Fengkai Zhang
PATRIC: The VBI PathoSystems Resource Integration Center. 401-406 - Alexei E. Kazakov, Michael J. Cipriano
RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. 407-412 - Kim Brügger
The Sulfolobus database. 413-415 - Chia-Hung Chang, Yu-Chung Chang, Anthony Underwood, Chien-Shun Chiou
VNTRDB: a bacterial variable number tandem repeat locus database. 416-421 - Bradley I. Arshinoff, Garret Suen
Xanthusbase: adapting wikipedia principles to a model organism database. 422-426 - Cristina Aurrecoechea, Mark Heiges, Haiming Wang, Zhiming Wang, Steve Fischer, Philippa M. Rhodes, John A. Miller
ApiDB: integrated resources for the apicomplexan bioinformatics resource center. 427-430 - Junichi Watanabe, Hiroyuki Wakaguri, Masahide Sasaki, Yutaka Suzuki, Sumio Sugano:
Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs. 431-438 - Olivier Arnaiz
ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. 439-444 - Emmet A. O'Brien, Liisa B. Koski
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). 445-451 - Martha B. Arnaud, Maria C. Costanzo, Marek S. Skrzypek, Prachi Shah, Gail Binkley, Christopher Lane, Stuart R. Miyasato, Gavin Sherlock
Sequence resources at the Candida Genome Database. 452-456 - Alexandre Gattiker, Christa Niederhauser-Wiederkehr, James Moore, Leandro Hermida
The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction. 457-462 - Luciano Fernandez-Ricaud
PROPHECY - a yeast phenome database, update 2006. 463-467 - Robert S. Nash, Shuai Weng, Benjamin C. Hitz, Rama Balakrishnan, Karen R. Christie
Expanded protein information at SGD: new pages and proteome browser. 468-471 - Lisa R. Girard, Tristan J. Fiedler, Todd W. Harris
WormBook: the online review of Caenorhabditis elegans biology. 472-475 - Liangjiang Wang, Suzhi Wang, Yonghua Li, Martin S. R. Paradesi, Susan J. Brown
BeetleBase: the model organism database for Tribolium castaneum. 476-479 - Donald G. Gilbert:
DroSpeGe: rapid access database for new Drosophila species genomes. 480-485 - Madeline A. Crosby, Joshua L. Goodman
FlyBase: genomes by the dozen. 486-491 - Thomas Horn, Zeynep Arziman, Juerg Berger, Michael Boutros
GenomeRNAi: a database for cell-based RNAi phenotypes. 492-497 - Christoph Dieterich, Waltraud Roeseler, Patrick Sobetzko, Ralf J. Sommer:
Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus. 498-502 - Daniel Lawson
VectorBase: a home for invertebrate vectors of human pathogens. 503-505 - Tamberlyn Bieri, Darin Blasiar, Philip Ozersky, Igor Antoshechkin, Carol Bastiani, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis
WormBase: new content and better access. 506-510 - Jens Barthelmes, Christian Ebeling
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. 511-514 - Gemma L. Holliday
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. 515-520 - David S. Wishart
HMDB: the Human Metabolome Database. 521-526 - Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward A. Dennis
LMSD: LIPID MAPS structure database. 527-532 - Claudia Choi, Richard Münch, Stefan Leupold, Johannes Klein, Inga Siegel, Bernhard Thielen, Beatrice Benkert, Martin Kucklick, Max Schobert, Jens Barthelmes, Christian Ebeling
SYSTOMONAS - an integrated database for systems biology analysis of Pseudomonas. 533-537 - H. Craig Mak, Mike Daly, Bianca Gruebel, Trey Ideker
CellCircuits: a database of protein network models. 538-545 - Yoshinobu Igarashi, Alexey M. Eroshkin, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang
CutDB: a proteolytic event database. 546-549 - Fedor A. Kolpakov
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. 550-556 - Arnaud Céol
DOMINO: a database of domain-peptide interactions. 557-560 - Samuel Kerrien
IntAct - open source resource for molecular interaction data. 561-565 - Magesh Jayapandian, Adriane Chapman, V. Glenn Tarcea, Cong Yu, Aaron Elkiss, Angela Ianni
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. 566-571 - Andrew Chatr-aryamontri, Arnaud Céol
MINT: the Molecular INTeraction database. 572-574 - Petras J. Kundrotas, Emil Alexov:
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. 575-579 - Emily R. Jefferson
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions. 580-589 - Gautam Chaurasia, Yasir Iqbal, Christian Hänig, Hanspeter Herzel, Erich E. Wanker
UniHI: an entry gate to the human protein interactome. 590-594 - Kieran Hervold, Andrew Martin, Roger A. Kirkpatrick, Paul F. Mc Kenna, F. A. Ramirez-Weber:
Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community. 595-598 - Fiona M. McCarthy
AgBase: a unified resource for functional analysis in agriculture. 599-603 - Zhi-Liang Hu, Eric Ryan Fritz, James M. Reecy
AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. 604-609 - Tim J. P. Hubbard, Bronwen L. Aken, Kathryn Beal, Benoît Ballester
Ensembl 2007. 610-617 - Constance M. Smith
The mouse Gene Expression Database (GXD): 2007 update. 618-623 - Raquel Egea
MamPol: a database of nucleotide polymorphism in the Mammalia class. 624-629 - Janan T. Eppig, Judith A. Blake
The mouse genome database (MGD): new features facilitating a model system. 630-637 - Dale A. Begley, Debra M. Krupke
Mouse Tumor Biology Database (MTB): status update and future directions. 638-642 - Molly A. Bogue, Stephen C. Grubb, Terry P. Maddatu, Carol J. Bult:
Mouse Phenome Database (MPD). 643-649 - Hirohide Uenishi, Tomoko Eguchi-Ogawa, Hiroki Shinkai, Naohiko Okumura, Kohei Suzuki, Daisuke Toki, Noriyuki Hamasima, Takashi Awata:
PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. 650-653 - Jue Ruan, Yiran Guo, Heng Li
PigGIS: Pig Genomic Informatics System. 654-657 - Simon N. Twigger
The Rat Genome Database, update 2007 - Easing the path from disease to data and back again. 658-662 - Daryl J. Thomas, Kate R. Rosenbloom, Hiram Clawson
The ENCODE Project at UC Santa Cruz. 663-667 - Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Heather Trumbower, Daryl J. Thomas, Archana Thakkapallayil, Charles W. Sugnet, Mario Stanke, Kayla E. Smith, Adam C. Siepel
The UCSC genome browser database: update 2007. 668-673 - Alecksandr Kutchma, Nayeem Quayum, Jan Jensen
GeneSpeed: protein domain organization of the transcriptome. 674-679 - Dongmei Zuo, Stephanie E. Mohr
PlasmID: a centralized repository for plasmid clone information and distribution. 680-684 - Koichiro Higasa, Katsuyuki Miyatake, Yoji Kukita
D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples. 685-689 - Sjozef van Baal, Polynikis Kaimakis
FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide. 690-695 - Philip Groth, Nadia Pavlova, Ivan Kalev, Spas Tonov, Georgi Georgiev, Hans-Dieter Pohlenz, Bertram Weiss:
PhenomicDB: a new cross-species genotype/phenotype resource. 696-699 - Anil G. Jegga
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. 700-706 - Shengting Li, Lijia Ma, Heng Li
Snap: an integrated SNP annotation platform. 707-710 - Jungsun Park, Sohyun Hwang, Yong Seok Lee, Sang-Cheol Kim, Doheon Lee
SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. 711-715 - Daryl J. Thomas, Heather Trumbower, Andrew D. Kern, Brooke L. Rhead, Robert M. Kuhn, David Haussler, W. James Kent:
Variation resources at UC Santa Cruz. 716-720 - Maureen E. Higgins, Martine Claremont, John E. Major, Chris Sander, Alex E. Lash
CancerGenes: a gene selection resource for cancer genome projects. 721-726 - Wen-Hui Su
OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci. 727-731 - Suisheng Tang, Zhuo Zhang, Sin Lam Tan, Man-Hung Eric Tang
KBERG: KnowledgeBase for Estrogen Responsive Genes. 732-736 - Wuxue Zhang, Yong Zhang, Hui Zheng, Chen Zhang, Wei Xiong, John G. Olyarchuk, Michael G. Walker, Weifeng Xu, Min Zhao
SynDB: a Synapse protein DataBase based on synapse ontology. 737-741 - Erin M. Hulbert, Luc J. Smink, Ellen C. Adlem, James E. Allen
T1DBase: integration and presentation of complex data for type 1 diabetes research. 742-746 - Helen E. Parkinson
ArrayExpress - a public database of microarray experiments and gene expression profiles. 747-750 - Joan M. Mazzarelli, John Brestelli, Regina K. Gorski, Junmin Liu, Elisabetta Manduchi, Deborah F. Pinney, Jonathan Schug, Peter White
EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. 751-755 - Fei Pan, Chi-Hsien Chiu, Sudip Pulapura, Michael R. Mehan, Juan Nunez-Iglesias
Gene Aging Nexus: a web database and data mining platform for microarray data on aging. 756-759 - Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Dmitry Rudnev, Carlos Evangelista, Irene F. Kim, Alexandra Soboleva, Maxim Tomashevsky, Ron Edgar
NCBI GEO: mining tens of millions of expression profiles - database and tools update. 760-765 - Janos Demeter
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. 766-770 - Yanling Zhang, Yong Zhang, Jun Adachi, Jesper V. Olsen
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes. 771-779 - Yi-Bu Chen, Ansuman Chattopadhyay
The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System - a one-stop gateway to online bioinformatics databases and software tools. 780-785 - Megan Sickmeier, Justin A. Hamilton, Tanguy LeGall, Vladimir Vacic
DisProt: the Database of Disordered Proteins. 786-793 - C. J. Zheng, Lianyi Han
PharmGED: Pharmacogenetic Effect Database. 794-799 - Alexander Loy
probeBase - an online resource for rRNA-targeted oligonucleotide probes: new features 2007. 800-804 - Wenwu Cui, Dennis D. Taub, Kevin Gardner:
qPrimerDepot: a primer database for quantitative real time PCR. 805-809 - Nuwee Wiwatwattana
Organelle DB: an updated resource of eukaryotic protein localization and function. 810-814 - Agatha Schlüter
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. 815-822 - Eduardo Ruiz-Pesini, Marie T. Lott
An enhanced MITOMAP with a global mtDNA mutational phylogeny. 823-828 - Cameron Johnson, Lewis Bowman, Alex T. Adai, Vicki Vance, Venkatesan Sundaresan
CSRDB: a small RNA integrated database and browser resource for cereals. 829-833 - Manuel Spannagl
MIPSPlantsDB - plant database resource for integrative and comparative plant genome research. 834-840 - Lorenz Bülow, Martin Schindler, Reinhard Hehl
PathoPlant®: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. 841-845 - Kevin L. Childs
The TIGR Plant Transcript Assemblies database. 846-851 - Nigel S. Walker, Nicholas Stiffler
POGs/PlantRBP: a resource for comparative genomics in plants. 852-856 - Claudia Galuschka, Martin Schindler, Lorenz Bülow, Reinhard Hehl
AthaMap web tools for the analysis and identification of co-regulated genes. 857-862 - Takeshi Obayashi, Kengo Kinoshita, Kenta Nakai, Masayuki Shibaoka, Shinpei Hayashi
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. 863-869 - Timothy A. Erwin
BASC: an integrated bioinformatics system for Brassica research. 870-873 - Yong Li
GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions. 874-878 - Huazong Zeng, Lijun Luo, Weixiong Zhang
PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information. 879-882 - Shu Ouyang, Wei Zhu, John A. Hamilton Jr.
The TIGR Rice Genome Annotation Resource: improvements and new features. 883-887 - Nathalie Pavy, James J. Johnson, John A. Crow, Charles Paule, Timothy M. Kunau, John MacKay
ForestTreeDB: a database dedicated to the mining of tree transcriptomes. 888-894 - Carolyn J. Lawrence
MaizeGDB's new data types, resources and activities. 895-900 - Nunzio D'Agostino
TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species. 901-905 - Stefan Günther, Dorothea Hempel, Mathias Dunkel
SuperHapten: a comprehensive database for small immunogenic compounds. 906-910
Volume 35, Number Web-Server-Issue, July 2007
- Gary Benson:
Editorial. 1
- Joanne A. Fox, Scott McMillan, B. F. Francis Ouellette
Conducting Research on the Web: 2007 Update for the Bioinformatics Links Directory. 3-5 - Alberto Labarga
Web Services at the European Bioinformatics Institute. 6-11 - Mounir Errami, Jonathan D. Wren
eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications. 12-15 - Ildefonso Cases
CARGO: a web portal to integrate customized biological information. 16-20 - José María Fernández
iHOP web services. 21-26 - Jake Gunn Glanville, Dan Kirshner
Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis. 27-32 - Thomas M. Keane
MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. 33-37 - Joaquín Tárraga, Ignacio Medina
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. 38-42 - Warren A. Kibbe
OligoCalc: an online oligonucleotide properties calculator. 43-46 - Peng Jiang
RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features. 47-51 - Ibtissem Grissa, Gilles Vergnaud
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. 52-57 - Roy Eric Collins
REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis. 58-62 - Ming-Fang Tsai, Yi-Jung Lin, Yu-Chang Cheng, Kuo-Hsi Lee, Cheng-Chih Huang, Yuan-Tsong Chen, Adam Yao:
PrimerZ: streamlined primer design for promoters, exons and human SNPs. 63-65 - Yung-fu Chen, Rung Ching Chen, Lin-Yu Tseng
NTMG (N-terminal Truncated Mutants Generator for cDNA): an automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants. 66-70 - Andreas Untergasser, Harm Nijveen
Primer3Plus, an enhanced web interface to Primer3. 71-74 - Ramón Díaz-Uriarte
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite. 75-80 - Lucía Conde
ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. 81-85 - Hubert Rehrauer
MAGMA: analysis of two-channel microarrays made easy. 86-90 - Fátima Al-Shahrour, Pablo Minguez
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. 91-96 - Hong-Yu Ou
MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. 97-104 - Yue Lu, Xin He, Sheng Zhong:
Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease. 105-114 - Deepak Grover, Alonzo S. Woodfield, Ranjana Verma, Peter P. Zandi, Douglas F. Levinson, James B. Potash:
QuickSNP: an automated web server for selection of tagSNPs. 115-120 - Hongkun Zheng, Junjie Shi, Xiaodong Fang, Yuan Li, Søren Vang, Wei Fan, Junyi Wang, Zhang Zhang, Wen Wang, Karsten Kristiansen, Jun Wang:
FGF: A web tool for Fishing Gene Family in a whole genome database. 121-125 - Pere Puigbò
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. 126-131 - Michael C. Angellotti, Shafquat B. Bhuiyan, Guorong Chen, Xiu-Feng Wan:
CodonO: codon usage bias analysis within and across genomes. 132-136 - Chun Liang, Gang Wang, Lin Liu, Guoli Ji, Yuansheng Liu, Jinqiao Chen, Jason S. Webb, Greg J. Reese, Jeffrey F. D. Dean
WebTraceMiner: a web service for processing and mining EST sequence trace files. 137-142 - Shivashankar H. Nagaraj, Nandan Deshpande, Robin B. Gasser
ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. 143-147 - Rowan A. C. Mitchell
Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence. 148-151 - Yan Zhang, Shiuh-Ming Luoh, Lawrence S. Hon, Robert Baertsch, William I. Wood, Zemin Zhang:
GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. 152-158 - Byungwook Lee, Taehui Hong, Sang Jin Byun, Taeha Woo, Yoon Jeong Choi:
ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences. 159-162 - Tomás Norambuena
SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation. 163-168 - Da Wei Huang, Brad T. Sherman, Qina Tan, Joseph Kir, David Liu, David Bryant, Yongjian Guo, Robert M. Stephens, Michael W. Baseler, H. Clifford Lane, Richard A. Lempicki
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. 169-175 - Nicolas Goffard, Georg Weiller:
PathExpress: a web-based tool to identify relevant pathways in gene expression data. 176-181 - Yuki Moriya
KAAS: an automatic genome annotation and pathway reconstruction server. 182-185 - Christina Backes, Andreas Keller
GeneTrail - advanced gene set enrichment analysis. 186-192 - Jüri Reimand
g: Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments. 193-200 - Christoph D. Schmid, Thierry Sengstag
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data. 201-205 - Purvesh Khatri
Onto-Tools: new additions and improvements in 2006. 206-211 - Carolina Perez-Iratxeta, Peer Bork
Update of the G2D tool for prioritization of gene candidates to inherited diseases. 212-216 - Katherine A. Romer, Guy-Richard Kayombya, Ernest Fraenkel
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches. 217-220 - Huai-Kuang Tsai
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. 221-226 - Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita
Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. 227-231 - William A. Thompson, Lee Aaron Newberg, Sean Conlan
The Gibbs Centroid Sampler. 232-237 - Li-Wei Chang, Burr R. Fontaine, Gary D. Stormo, Rakesh Nagarajan:
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis. 238-244 - Shannan J. Ho Sui, Debra L. Fulton, David J. Arenillas, Andrew T. Kwon
oPOSSUM: integrated tools for analysis of regulatory motif over-representation. 245-252 - Shaun Mahony
STAMP: a web tool for exploring DNA-binding motif similarities. 253-258 - Jonathan M. Carlson, Arijit Chakravarty, Charles E. DeZiel, Robert H. Gross:
SCOPE: a web server for practical de novo motif discovery. 259-264 - Zhao Xu, Hao Wang
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. 265-268 - Jean-François Lucier, Jonathan Perreault
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures. 269-274 - Guoqing Lu, Thaine W. Rowley, Rebecca Garten, Ruben O. Donis:
FluGenome: a web tool for genotyping influenza A virus. 275-279 - Yiming Bao
FLAN: a web server for influenza virus genome annotation. 280-284 - Rezarta Islamaj Dogan
SplicePort - An interactive splice-site analysis tool. 285-291 - Zoé Lacroix, Christophe Legendre, Louiqa Raschid, Ben Snyder:
BIPASS: BioInformatics Pipeline Alternative Splicing Services. 292-296 - Sylvain Foissac
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. 297-299 - Mugdha Khaladkar, Vivian Bellofatto, Jason Tsong-Li Wang, Bin Tian
RADAR: a web server for RNA data analysis and research. 300-304 - Eva Freyhult, Vincent Moulton
RNAbor: a web server for RNA structural neighbors. 305-309 - Anke Busch, Rolf Backofen:
INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints. 310-313 - Wenjie Shu
RSRE: RNA structural robustness evaluator. 314-319 - Jens Reeder, Peter Steffen, Robert Giegerich:
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows. 320-324 - Cagri Aksay, Raheleh Salari, Emre Karakoç, Can Alkan
taveRNA: a web suite for RNA algorithms and applications. 325-329 - Alexander Kaiser, Jan Krüger, Dirk Evers:
RNA Movies 2: sequential animation of RNA secondary structures. 330-334 - Andreas R. Gruber
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. 335-338 - Peng Jiang
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. 339-344 - Lei Kong, Yong Zhang, Zhi-Qiang Ye
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. 345-349 - Helena Tåquist, Yuanyuan Cui, David H. Ardell:
TFAM 1.0: an online tRNA function classifier. 350-353 - Jianlin Cheng
DOMAC: an accurate, hybrid protein domain prediction server. 354-356 - Harianto Tjong, Sanbo Qin
PI2PE: protein interface/interior prediction engine. 357-362 - Narcis Fernandez-Fuentes
M4T: a comparative protein structure modeling server. 363-368 - Björn Wallner
Pcons.net: protein structure prediction meta server. 369-374 - Ian W. Davis, Andrew Leaver-Fay, Vincent B. Chen, Jeremy N. Block, Gary J. Kapral, Xueyi Wang, Laura Weston Murray, W. Bryan Arendall III, Jack Snoeyink
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. 375-383 - Alper Uzun
Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. 384-392 - Marc A. Martí-Renom
DBAli tools: mining the protein structure space. 393-397 - Kengo Kinoshita, Yoichi Murakami, Haruki Nakamura:
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. 398-402 - Christian X. Weichenberger
NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures. 403-406 - Markus Wiederstein
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. 407-410 - Stefan J. Suhrer, Markus Gruber, Manfred J. Sippl:
QSCOP-BLAST - fast retrieval of quantified structural information for protein sequences of unknown structure. 411-415 - Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. 416-419 - Yan-Long Lai, Shih-Chung Yen, Sung-Huan Yu
pKNOT: the protein KNOT web server. 420-424 - Grigory Kolesov, Peter Virnau, Mehran Kardar
Protein knot server: detection of knots in protein structures. 425-428 - Lukas Käll
Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. 429-432 - Marco Pagni
MyHits: improvements to an interactive resource for analyzing protein sequences. 433-437 - Chi-Hua Tung
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. 438-443 - Coral del Val
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. 444-450 - Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
SH3-Hunter: discovery of SH3 domain interaction sites in proteins. 451-454 - Norman E. Davey
The SLiMDisc server: short, linear motif discovery in proteins. 455-459 - Takashi Ishida
PrDOS: prediction of disordered protein regions from amino acid sequence. 460-464 - Chung-Tsai Su, Chien-Yu Chen
iPDA: integrated protein disorder analyzer. 465-472 - K. G. Tina, Rana Bhadra, Narayanaswamy Srinivasan:
PIC: Protein Interactions Calculator. 473-476 - Joel Franklin, Patrice Koehl
MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. 477-482 - Ludovic Autin, Pierre Tufféry
PMG: online generation of high-quality molecular pictures and storyboarded animations. 483-488 - C. Axel Innis
siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins. 489-494 - K. Anton Feenstra
Sequence harmony: detecting functional specificity from alignments. 495-498 - Harpreet Kaur Saini
FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments. 499-502 - Kshama Goyal, Debasisa Mohanty
PAR-3D: a server to predict protein active site residues. 503-505 - Adi Stern, Adi Doron-Faigenboim, Elana Erez, Eric Martz
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. 506-511 - Clifford E. Felder, Jaime Prilusky, Israel Silman, Joel L. Sussman
A server and database for dipole moments of proteins. 512-521 - Todd J. Dolinsky, Paul Czodrowski
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. 522-525 - Shula Shazman, Gershon Celniker, Omer Haber, Fabian Glaser, Yael Mandel-Gutfreund
Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces. 526-530 - Mark V. Berjanskii, David S. Wishart
The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. 531-537 - Jinrui Xu
CytoSVM: an advanced server for identification of cytokine-receptor interactions. 538-542 - Hani Neuvirth, Uri Heinemann, David Birnbaum, Naftali Tishby, Gideon Schreiber:
ProMateus - an open research approach to protein-binding sites analysis. 543-548 - Narendra Kumar
MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. 549-555 - P. Christoph Champ, Carlos J. Camacho:
FastContact: a free energy scoring tool for protein-protein complex structures. 556-560 - Yung-Chiang Chen, Yu-Shu Lo, Wen-Chang Hsu, Jinn-Moon Yang
3D-partner: a web server to infer interacting partners and binding models. 561-567 - T. Bohme Leite, D. Gomes, Maria A. Miteva
Frog: a FRee Online druG 3D conformation generator. 568-572 - Gonzalo López
firestar - prediction of functionally important residues using structural templates and alignment reliability. 573-577 - Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. 578-584 - Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C. J. Adams-Collier, Kenta Nakai:
WoLF PSORT: protein localization predictor. 585-587 - Yung-Hao Wong, Tzong-Yi Lee, Han-Kuen Liang, Chia-Mao Huang, Ting-Yuan Wang, Yi-Huan Yang, Chia-Huei Chu, Hsien-Da Huang, Ming-Tat Ko, Jenn-Kang Hwang:
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. 588-594 - Joshua S. Kaminker, Yan Zhang, Colin K. Watanabe, Zemin Zhang:
CanPredict: a computational tool for predicting cancer-associated missense mutations. 595-598 - Jeffry D. Sander, Peter Zaback
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. 599-605 - Eoin Fahy, Manish Sud, Dawn Cotter, Shankar Subramaniam:
LIPID MAPS online tools for lipid research. 606-612 - Thomas Handorf, Oliver Ebenhöh
MetaPath Online: a web server implementation of the network expansion algorithm. 613-618 - Jost Degenhardt, Martin Haubrock
DEEP - A tool for differential expression effector prediction. 619-624 - Zhenjun Hu, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. 625-632 - Feng-Chi Chen, Chuang-Jong Chen, Trees-Juen Chuang
INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events. 633-638 - Yun Sheng Chung, Wei-Hsun Lee, Chuan Yi Tang, Chin Lung Lu:
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints. 639-644 - Sébastien Moretti
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. 645-648 - Jimin Pei, Bong-Hyun Kim, Ming Tang, Nick V. Grishin:
PROMALS web server for accurate multiple protein sequence alignments. 649-652 - Ruslan Sadreyev, Ming Tang, Bong-Hyun Kim, Nick V. Grishin:
COMPASS server for remote homology inference. 653-658 - Fabrizio Ferrè
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. 659-668 - Michael Brudno, Alexander Poliakov, Simon Minovitsky, Igor Ratnere, Inna Dubchak:
Multiple whole genome alignments and novel biomedical applications at the VISTA portal. 669-674 - Satish Chikkagoudar
eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities. 675-677 - Yi Zhou, Laura F. Landweber:
BLASTO: a tool for searching orthologous groups. 678-682 - Andreas Keller
SePaCS - a web-based application for classification of seroreactivity profiles. 683-687 - Swetlana Nikolajewa, Rainer Pudimat, Michael Hiller, Matthias Platzer, Rolf Backofen:
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data. 688-693 - Alvaro Martinez Barrio, Daniel Soeria-Atmadja, Anders Nistér, Mats G. Gustafsson, Ulf Hammerling, Erik Bongcam-Rudloff:
EVALLER: a web server for in silico assessment of potential protein allergenicity. 694-700 - Leonid Zamdborg, Richard D. LeDuc
ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry. 701-706 - Chuan-Yih Yu, Yin-Hao Tsui, Yi-Hwa Yian, Ting-Yi Sung, Wen-Lian Hsu:
The Multi-Q web server for multiplexed protein quantitation. 707-712 - Sik Lok Lam
DSHIFT: a web server for predicting DNA chemical shifts. 713-717 - Trias Thireou
CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography. 718-722
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