Nucleic Acids Research

Editorial

Alex Bateman

Editorial
Nucl. Acids Res. 2008 36: D1; doi:10.1093/nar/gkm1139 [Extract] [FREE Full Text] [Print PDF][Screen PDF]  

Articles

Get checked abstract Michael Y. Galperin

The Molecular Biology Database Collection: 2008 update
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D2-D4; doi:10.1093/nar/gkm1037 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Database Summaries]  

Get checked abstract Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim Hubbard, and Ewan Birney

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
Nucleic Acids Research Advance Access published on November 26, 2007
Nucl. Acids Res. 2008 36: D5-D12; doi:10.1093/nar/gkm1018 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y. Geer, Wolfgang Helmberg, Yuri Kapustin, Oleg Khovayko, David Landsman, David J. Lipman, Thomas L. Madden, Donna R. Maglott, Vadim Miller, James Ostell, Kim D. Pruitt, Gregory D. Schuler, Martin Shumway, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, and Eugene Yaschenko

Database resources of the National Center for Biotechnology Information
Nucleic Acids Research Advance Access published on November 27, 2007
Nucl. Acids Res. 2008 36: D13-D21; doi:10.1093/nar/gkm1000 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract H. Sugawara, O. Ogasawara, K. Okubo, T. Gojobori, and Y. Tateno

DDBJ with new system and face
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D22-D24; doi:10.1093/nar/gkm889 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler

GenBank
Nucleic Acids Research Advance Access published on December 11, 2007
Nucl. Acids Res. 2008 36: D25-D30; doi:10.1093/nar/gkm929 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Yu Zhou, Chen Lu, Qi-Jia Wu, Yu Wang, Zhi-Tao Sun, Jia-Cong Deng, and Yi Zhang

GISSD: Group I Intron Sequence and Structure Database
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D31-D37; doi:10.1093/nar/gkm766 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract C. Lloréns, R. Futami, D. Bezemer, and A. Moya

The Gypsy Database (GyDB) of mobile genetic elements
Nucleic Acids Research Advance Access published on September 25, 2007
Nucl. Acids Res. 2008 36: D38-D46; doi:10.1093/nar/gkm697 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Asaf Levy, Noa Sela, and Gil Ast

TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D47-D52; doi:10.1093/nar/gkm949 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Veenu Aishwarya and P. C. Sharma

UgMicroSatdb: database for mining microsatellites from unigenes
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D53-D56; doi:10.1093/nar/gkm811 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Marco Mangone, Philip MacMenamin, Charles Zegar, Fabio Piano, and Kristin C. Gunsalus

UTRome.org: a platform for 3'UTR biology in C. elegans
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D57-D62; doi:10.1093/nar/gkm946 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast, and Ralf Zimmer

ProSAS: a database for analyzing alternative splicing in the context of protein structures
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D63-D68; doi:10.1093/nar/gkm793 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Amrita Pati, Ying Jin, Karsten Klage, Richard F. Helm, Lenwood S. Heath, and Naren Ramakrishnan

CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D69-D76; doi:10.1093/nar/gkm804 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Takeshi Obayashi, Shinpei Hayashi, Masayuki Shibaoka, Motoshi Saeki, Hiroyuki Ohta, and Kengo Kinoshita

COXPRESdb: a database of coexpressed gene networks in mammals
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D77-D82; doi:10.1093/nar/gkm840 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Lei Bao, Mi Zhou, and Yan Cui

CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D83-D87; doi:10.1093/nar/gkm875 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Derek Wilson, Varodom Charoensawan, Sarah K. Kummerfeld, and Sarah A. Teichmann

DBD––taxonomically broad transcription factor predictions: new content and functionality
Nucleic Acids Research Advance Access published on December 11, 2007
Nucl. Acids Res. 2008 36: D88-D92; doi:10.1093/nar/gkm964 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Nicolas Sierro, Yuko Makita, Michiel de Hoon, and Kenta Nakai

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D93-D96; doi:10.1093/nar/gkm910 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, and Kenta Nakai

DBTSS: database of transcription start sites, progress report 2008
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D97-D101; doi:10.1093/nar/gkm901 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jan Christian Bryne, Eivind Valen, Man-Hung Eric Tang, Troels Marstrand, Ole Winther, Isabelle da Piedade, Anders Krogh, Boris Lenhard, and Albin Sandelin

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update
Nucleic Acids Research Advance Access published on November 15, 2007
Nucl. Acids Res. 2008 36: D102-D106; doi:10.1093/nar/gkm955 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Obi L. Griffith, Stephen B. Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth Wasserman, Ross Hardison, Casey M. Bergman, Steven J.M. Jones, and The Open Regulatory Annotation Consortium

ORegAnno: an open-access community-driven resource for regulatory annotation
Nucleic Acids Research Advance Access published on November 15, 2007
Nucl. Acids Res. 2008 36: D107-D113; doi:10.1093/nar/gkm967 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Gang-Qing Hu, Xiaobin Zheng, Yi-Fan Yang, Philippe Ortet, Zhen-Su She, and Huaiqiu Zhu

ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D114-D119; doi:10.1093/nar/gkm799 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Socorro Gama-Castro, Verónica Jiménez-Jacinto, Martín Peralta-Gil, Alberto Santos-Zavaleta, Mónica I. Peñaloza-Spinola, Bruno Contreras-Moreira, Juan Segura-Salazar, Luis Muñiz-Rascado, Irma Martínez-Flores, Heladia Salgado, César Bonavides-Martínez, Cei Abreu-Goodger, Carlos Rodríguez-Penagos, Juan Miranda-Ríos, Enrique Morett, Enrique Merino, Araceli M. Huerta, Luis Treviño-Quintanilla, and Julio Collado-Vides

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
Nucleic Acids Research Advance Access published on December 23, 2007
Nucl. Acids Res. 2008 36: D120-D124; doi:10.1093/nar/gkm994 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Barrett C. Foat, Ronald G. Tepper, and Harmen J. Bussemaker

TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D125-D131; doi:10.1093/nar/gkm828 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Pedro T. Monteiro, Nuno D. Mendes, Miguel C. Teixeira, Sofia d’Orey, Sandra Tenreiro, Nuno P. Mira, Hélio Pais, Alexandre P. Francisco, Alexandra M. Carvalho, Artur B. Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira, and Ana T. Freitas

YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: D132-D136; doi:10.1093/nar/gkm976 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Anason S. Halees, Rashad El-Badrawi, and Khalid S. A. Khabar

ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D137-D140; doi:10.1093/nar/gkm959 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Oleg Kikin, Zachary Zappala, Lawrence D’Antonio, and Paramjeet S. Bagga

GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs
Nucleic Acids Research Advance Access published on November 27, 2007
Nucl. Acids Res. 2008 36: D141-D148; doi:10.1093/nar/gkm982 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Doron Betel, Manda Wilson, Aaron Gabow, Debora S. Marks, and Chris Sander

The microRNA.org resource: targets and expression
Nucleic Acids Research Advance Access published on December 23, 2007
Nucl. Acids Res. 2008 36: D149-D153; doi:10.1093/nar/gkm995 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sam Griffiths-Jones, Harpreet Kaur Saini, Stijn van Dongen, and Anton J. Enright

miRBase: tools for microRNA genomics
Nucleic Acids Research Advance Access published on November 8, 2007
Nucl. Acids Res. 2008 36: D154-D158; doi:10.1093/nar/gkm952 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Seungyoon Nam, Bumjin Kim, Seokmin Shin, and Sanghyuk Lee

miRGator: an integrated system for functional annotation of microRNAs
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D159-D164; doi:10.1093/nar/gkm829 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sheng-Da Hsu, Chia-Huei Chu, Ann-Ping Tsou, Shu-Jen Chen, Hua-Chien Chen, Paul Wei-Che Hsu, Yung-Hao Wong, Yi-Hsuan Chen, Gian-Hung Chen, and Hsien-Da Huang

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D165-D169; doi:10.1093/nar/gkm1012 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, and Runsheng Chen

NONCODE v2.0: decoding the non-coding
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D170-D172; doi:10.1093/nar/gkm1011 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract S. Sai Lakshmi and Shipra Agrawal

piRNABank: a web resource on classified and clustered Piwi-interacting RNAs
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2008 36: D173-D177; doi:10.1093/nar/gkm696 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Dorota Piekna-Przybylska, Wayne A. Decatur, and Maurille J. Fournier

The 3D rRNA modification maps database: with interactive tools for ribosome analysis
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D178-D183; doi:10.1093/nar/gkm855 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sung-Chou Li, Cheng-Kai Shiau, and Wen-chang Lin

Vir-Mir db: prediction of viral microRNA candidate hairpins
Nucleic Acids Research Advance Access published on August 15, 2007
Nucl. Acids Res. 2008 36: D184-D189; doi:10.1093/nar/gkm610 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract The UniProt Consortium

The Universal Protein Resource (UniProt)
Nucleic Acids Research Advance Access published on November 27, 2007
Nucl. Acids Res. 2008 36: D190-D195; doi:10.1093/nar/gkm895 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract H. W. Mewes, S. Dietmann, D. Frishman, R. Gregory, G. Mannhaupt, K. F. X. Mayer, M. Münsterkötter, A. Ruepp, M. Spannagl, V. Stümpflen, and T. Rattei

MIPS: analysis and annotation of genome information in 2007
Nucleic Acids Research Advance Access published on December 23, 2007
Nucl. Acids Res. 2008 36: D196-D201; doi:10.1093/nar/gkm980 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Shuichi Kawashima, Piotr Pokarowski, Maria Pokarowska, Andrzej Kolinski, Toshiaki Katayama, and Minoru Kanehisa

AAindex: amino acid index database, progress report 2008
Nucleic Acids Research Advance Access published on November 12, 2007
Nucl. Acids Res. 2008 36: D202-D205; doi:10.1093/nar/gkm998 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Conan K. L. Wang, Quentin Kaas, Laurent Chiche, and David J. Craik

CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D206-D210; doi:10.1093/nar/gkm953 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Hua Cheng, Bong-Hyun Kim, and Nick V. Grishin

MALISAM: a database of structurally analogous motifs in proteins
Nucleic Acids Research Advance Access published on September 12, 2007
Nucl. Acids Res. 2008 36: D211-D217; doi:10.1093/nar/gkm698 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ganesan Pugalenthi, P. N. Suganthan, R. Sowdhamini, and Saikat Chakrabarti

MegaMotifBase: a database of structural motifs in protein families and superfamilies
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D218-D221; doi:10.1093/nar/gkm794 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract David S. Wishart, David Arndt, Mark Berjanskii, An Chi Guo, Yi Shi, Savita Shrivastava, Jianjun Zhou, You Zhou, and Guohui Lin

PPT-DB: the protein property prediction and testing database
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2008 36: D222-D229; doi:10.1093/nar/gkm800 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Josefine Sprenger, J. Lynn Fink, Seetha Karunaratne, Kelly Hanson, Nicholas A. Hamilton, and Rohan D. Teasdale

LOCATE: a mammalian protein subcellular localization database
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D230-D233; doi:10.1093/nar/gkm950 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Gábor E. Tusnády, Lajos Kalmár, and István Simon

TOPDB: topology data bank of transmembrane proteins
Nucleic Acids Research Advance Access published on October 5, 2007
Nucl. Acids Res. 2008 36: D234-D239; doi:10.1093/nar/gkm751 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Francesca Diella, Cathryn M. Gould, Claudia Chica, Allegra Via, and Toby J. Gibson

Phospho.ELM: a database of phosphorylation sites—update 2008
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D240-D244; doi:10.1093/nar/gkm772 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Béatrice A. Cuche, Edouard de Castro, Corinne Lachaize, Petra S. Langendijk-Genevaux, and Christian J. A. Sigrist

The 20 years of PROSITE
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2008 36: D245-D249; doi:10.1093/nar/gkm977 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Lars Juhl Jensen, Philippe Julien, Michael Kuhn, Christian von Mering, Jean Muller, Tobias Doerks, and Peer Bork

eggNOG: automated construction and annotation of orthologous groups of genes
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D250-D254; doi:10.1093/nar/gkm796 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang, and Yixue Li

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D255-D262; doi:10.1093/nar/gkm924 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ann-Charlotte Berglund, Erik Sjölund, Gabriel Östlund, and Erik L. L. Sonnhammer

InParanoid 6: eukaryotic ortholog clusters with inparalogs
Nucleic Acids Research Advance Access published on November 30, 2007
Nucl. Acids Res. 2008 36: D263-D266; doi:10.1093/nar/gkm1020 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Andreas Heger and Chris P. Ponting

OPTIC: orthologous and paralogous transcripts in clades
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D267-D270; doi:10.1093/nar/gkm852 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Evgenia V. Kriventseva, Nazim Rahman, Octavio Espinosa, and Evgeny M. Zdobnov

OrthoDB: the hierarchical catalog of eukaryotic orthologs
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D271-D275; doi:10.1093/nar/gkm845 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Andreas Heger, Eija Korpelainen, Taavi Hupponen, Kimmo Mattila, Vesa Ollikainen, and Liisa Holm

PairsDB atlas of protein sequence space
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D276-D280; doi:10.1093/nar/gkm879 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-Rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, and Alex Bateman

The Pfam protein families database
Nucleic Acids Research Advance Access published on November 26, 2007
Nucl. Acids Res. 2008 36: D281-D288; doi:10.1093/nar/gkm960 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Thomas Rattei, Patrick Tischler, Roland Arnold, Franz Hamberger, Jörg Krebs, Jan Krumsiek, Benedikt Wachinger, Volker Stümpflen, and Werner Mewes

SIMAP—structuring the network of protein similarities
Nucleic Acids Research Advance Access published on November 23, 2007
Nucl. Acids Res. 2008 36: D289-D292; doi:10.1093/nar/gkm963 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Quan-Yuan He, Quan-Ze He, Xing-Can Deng, Lei Yao, Er Meng, Zhong-Hua Liu, and Song-Ping Liang

ATDB: a uni-database platform for animal toxins
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D293-D297; doi:10.1093/nar/gkm832 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Karla Gendler, Tara Paulsen, and Carolyn Napoli

ChromDB: The Chromatin Database
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D298-D302; doi:10.1093/nar/gkm768 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jianwen Fang, Yinghua Dong, Nazila Salamat-Miller, and C. Russell Middaugh

DB-PABP: a database of polyanion-binding proteins
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2008 36: D303-D306; doi:10.1093/nar/gkm784 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Charles J. Reedy, Margaret M. Elvekrog, and Brian R. Gibney

Development of a heme protein structure–electrochemical function database
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D307-D313; doi:10.1093/nar/gkm814 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jérôme Gracy, Dung Le-Nguyen, Jean-Christophe Gelly, Quentin Kaas, Annie Heitz, and Laurent Chiche

KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D314-D319; doi:10.1093/nar/gkm939 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Neil D. Rawlings, Fraser R. Morton, Chai Yin Kok, Jun Kong, and Alan J. Barrett

MEROPS: the peptidase database
Nucleic Acids Research Advance Access published on November 8, 2007
Nucl. Acids Res. 2008 36: D320-D325; doi:10.1093/nar/gkm954 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ségolène Caboche, Maude Pupin, Valérie Leclère, Arnaud Fontaine, Philippe Jacques, and Gregory Kucherov

NORINE: a database of nonribosomal peptides
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2008 36: D326-D331; doi:10.1093/nar/gkm792 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sergi Castellano, Vadim N. Gladyshev, Roderic Guigó, and Marla J. Berry

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements
Nucleic Acids Research Advance Access published on January 3, 2008
Nucl. Acids Res. 2008 36: D332-D338; doi:10.1093/nar/gkm731 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Joshua D. Podlevsky, Christopher J. Bley, Rebecca V. Omana, Xiaodong Qi, and Julian J.-L. Chen

The Telomerase Database
Nucleic Acids Research Advance Access published on December 11, 2007
Nucl. Acids Res. 2008 36: D339-D343; doi:10.1093/nar/gkm700 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcántara, Michael Darsow, Mickaël Guedj, and Michael Ashburner

ChEBI: a database and ontology for chemical entities of biological interest
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D344-D350; doi:10.1093/nar/gkm791 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kathleen Petri Seiler, Gregory A. George, Mary Pat Happ, Nicole E. Bodycombe, Hyman A. Carrinski, Stephanie Norton, Steve Brudz, John P. Sullivan, Jeremy Muhlich, Martin Serrano, Paul Ferraiolo, Nicola J. Tolliday, Stuart L. Schreiber, *, and Paul A. Clemons

ChemBank: a small-molecule screening and cheminformatics resource database
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D351-D359; doi:10.1093/nar/gkm843 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract François-Yves Dupradeau, Christine Cézard, Rodolphe Lelong, Élodie Stanislawiak, Julien Pêcher, Jean Charles Delepine, and Piotr Cieplak

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D360-D367; doi:10.1093/nar/gkm887 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Taku Nakahara, Ryo Hashimoto, Hiroaki Nakagawa, Kenji Monde, Nobuaki Miura, and Shin-Ichiro Nishimura

Glycoconjugate Data Bank:Structures—an annotated glycan structure database and N-glycan primary structure verification service
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D368-D371; doi:10.1093/nar/gkm833 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ren Zhang, Yan Lin, and Chun-Ting Zhang

Greglist: a database listing potential G-quadruplex regulated genes
Nucleic Acids Research Advance Access published on October 4, 2007
Nucl. Acids Res. 2008 36: D372-D376; doi:10.1093/nar/gkm787 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Christian Selig, Matthias Wolf, Tobias Müller, Thomas Dandekar, and Jörg Schultz

The ITS2 Database II: homology modelling RNA structure for molecular systematics
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D377-D380; doi:10.1093/nar/gkm827 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Vinod Kumar Yadav, James Kappukalayil Abraham, Prithvi Mani, Rashi Kulshrestha, and Shantanu Chowdhury

QuadBase: genome-wide database of G4 DNA—occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D381-D385; doi:10.1093/nar/gkm781 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Mariusz Popenda, Marek Blazewicz, Marta Szachniuk, and Ryszard W. Adamiak

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
Nucleic Acids Research Advance Access published on October 5, 2007
Nucl. Acids Res. 2008 36: D386-D391; doi:10.1093/nar/gkm786 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Eckart Bindewald, Robert Hayes, Yaroslava G. Yingling, Wojciech Kasprzak, and Bruce A. Shapiro

RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D392-D397; doi:10.1093/nar/gkm842 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Fabian Birzele, Jan E. Gewehr, and Ralf Zimmer

AutoPSI: a database for automatic structural classification of protein sequences and structures
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D398-D401; doi:10.1093/nar/gkm834 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, and John L. Markley

BioMagResBank
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D402-D408; doi:10.1093/nar/gkm957 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Hidetoshi Kono, Tomo Yuasa, Shinya Nishiue, and Kei Yura

coliSNP database server mapping nsSNPs on protein structures
Nucleic Acids Research Advance Access published on October 5, 2007
Nucl. Acids Res. 2008 36: D409-D413; doi:10.1093/nar/gkm801 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Corin Yeats, Jonathan Lees, Adam Reid, Paul Kellam, Nigel Martin, Xinhui Liu, and Christine Orengo

Gene3D: comprehensive structural and functional annotation of genomes
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: D414-D418; doi:10.1093/nar/gkm1019 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Antonina Andreeva, Dave Howorth, John-Marc Chandonia, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, and Alexey G. Murzin

Data growth and its impact on the SCOP database: new developments
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D419-D425; doi:10.1093/nar/gkm993 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Kim Henrick, Zukang Feng, Wolfgang F. Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson, John L. Markley, Haruki Nakamura, Richard Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim Vranken, John Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, and Helen M. Berman

Remediation of the protein data bank archive
Nucleic Acids Research Advance Access published on December 11, 2007
Nucl. Acids Res. 2008 36: D426-D433; doi:10.1093/nar/gkm937 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Andreas Schlicker and Mario Albrecht

FunSimMat: a comprehensive functional similarity database
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D434-D439; doi:10.1093/nar/gkm806 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract The Gene Ontology Consortium

The Gene Ontology project in 2008
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D440-D444; doi:10.1093/nar/gkm883 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Elspeth A. Bruford, Michael J. Lush, Mathew W. Wright, Tam P. Sneddon, Sue Povey, and Ewan Birney

The HGNC Database in 2008: a resource for the human genome
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D445-D448; doi:10.1093/nar/gkm881 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Martin M Sachs, Mary Schaeffer, Lincoln Stein, Peter Stevens, Leszek Vincent, Felipe Zapata, and Doreen Ware

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
Nucl. Acids Res. 2008 36: D449-D454; doi:10.1093/nar/gkm908 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract In Seok Yang, Chunsun Ryu, Ki Joon Cho, Jin Kwang Kim, Swee Hoe Ong, Wayne P. Mitchell, Bong Su Kim, Hee-Bok Oh, and Kyung Hyun Kim

IDBD: Infectious Disease Biomarker Database
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2008 36: D455-D460; doi:10.1093/nar/gkm925 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Nicolas J. Tourasse and Anne-Brit Kolstø

SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis)
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2008 36: D461-D468; doi:10.1093/nar/gkm877 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Pierre Lechat, Laurence Hummel, Sandrine Rousseau, and Ivan Moszer

GenoList: an integrated environment for comparative analysis of microbial genomes
Nucleic Acids Research Advance Access published on November 21, 2007
Nucl. Acids Res. 2008 36: D469-D474; doi:10.1093/nar/gkm1042 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis, and Nikos C. Kyrpides

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D475-D479; doi:10.1093/nar/gkm884 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Toshiaki Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, and Yoshihiro Yamanishi

KEGG for linking genomes to life and the environment
Nucleic Acids Research Advance Access published on December 12, 2007
Nucl. Acids Res. 2008 36: D480-D484; doi:10.1093/nar/gkm882 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Emmanuel Courcelle, Yoann Beausse, Sébastien Letort, Olivier Stahl, Romain Fremez, Catherine Ngom-Bru, Jérôme Gouzy, and Thomas Faraut

Narcisse: a mirror view of conserved syntenies
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D485-D490; doi:10.1093/nar/gkm805 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, and Toni Gabaldón

PhylomeDB: a database for genome-wide collections of gene phylogenies
Nucleic Acids Research Advance Access published on October 25, 2007
Nucl. Acids Res. 2008 36: D491-D496; doi:10.1093/nar/gkm899 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Burke Squires, Catherine Macken, Adolfo Garcia-Sastre, Shubhada Godbole, Jyothi Noronha, Victoria Hunt, Roger Chang, Christopher N. Larsen, Ed Klem, Kevin Biersack, and Richard H. Scheuermann

BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence
Nucleic Acids Research Advance Access published on October 26, 2007
Nucl. Acids Res. 2008 36: D497-D503; doi:10.1093/nar/gkm905 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Yi Huang, Susanna K. P. Lau, Patrick C. Y. Woo, and Kwok-yung Yuen

CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2008 36: D504-D511; doi:10.1093/nar/gkm754 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Carla Kuiken, Peter Hraber, James Thurmond, and Karina Yusim

The hepatitis C sequence database in Los Alamos
Nucleic Acids Research Advance Access published on November 19, 2007
Nucl. Acids Res. 2008 36: D512-D516; doi:10.1093/nar/gkm962 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Inti Pedroso, Gustavo Rivera, Felipe Lazo, Max Chacón, Francisco Ossandón, Felipe A. Veloso, and David S. Holmes

AlterORF: a database of alternate open reading frames
Nucleic Acids Research Advance Access published on December 20, 2007
Nucl. Acids Res. 2008 36: D517-D518; doi:10.1093/nar/gkm886 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jeremy D. Glasner, Guy Plunkett, III, Bradley D. Anderson, David J. Baumler, Bryan S. Biehl, Valerie Burland, Eric L. Cabot, Aaron E. Darling, Bob Mau, Eric C. Neeno-Eckwall, David Pot, Yu Qiu, Anna I. Rissman, Sara Worzella, Sam Zaremba, Joel Fedorko, Tom Hampton, Paul Liss, Michael Rusch, Matthew Shaker, Lorie Shaull, Panna Shetty, Silpa Thotakura, Jon Whitmore, Frederick R. Blattner, John M. Greene, and Nicole T. Perna

Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D519-D523; doi:10.1093/nar/gkm973 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Pere Puigbò, Antoni Romeu, and Santiago Garcia-Vallvé

HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D524-D527; doi:10.1093/nar/gkm831 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Natalia N. Ivanova, and Nikos C. Kyrpides

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions
Nucleic Acids Research Advance Access published on October 12, 2007
Nucl. Acids Res. 2008 36: D528-D533; doi:10.1093/nar/gkm846 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Victor M. Markowitz, Natalia N. Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I-Min A. Chen, Yuri Grechkin, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavromatis, Philip Hugenholtz, and Nikos C. Kyrpides

IMG/M: a data management and analysis system for metagenomes
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D534-D538; doi:10.1093/nar/gkm869 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jian Yang, Lihong Chen, Lilian Sun, Jun Yu, and Qi Jin

VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics
Nucleic Acids Research Advance Access published on November 4, 2007
Nucl. Acids Res. 2008 36: D539-D542; doi:10.1093/nar/gkm951 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Roy R. Chaudhuri, Nicholas J. Loman, Lori A.S. Snyder, Christopher M. Bailey, Dov J. Stekel, and Mark J. Pallen

xBASE2: a comprehensive resource for comparative bacterial genomics
Nucleic Acids Research Advance Access published on November 5, 2007
Nucl. Acids Res. 2008 36: D543-D546; doi:10.1093/nar/gkm928 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Alberto M. R. Dávila, Pablo N. Mendes, Glauber Wagner, Diogo A. Tschoeke, Rafael R. C. Cuadrat, Felipe Liberman, Luciana Matos, Thiago Satake, Kary A. C. S. Ocaña, Omar Triana, Sérgio M. S. Cruz, Henrique C. L. Jucá, Juliano C. Cury, Fabricio N. Silva, Guilherme A. Geronimo, Margarita Ruiz, Eduardo Ruback, Floriano P. Silva, Jr, Christian M. Probst, Edmundo C. Grisard, Marco A. Krieger, Samuel Goldenberg, Maria C. R. Cavalcanti, Milton O. Moraes, Maria L. M. Campos, and Marta Mattoso

ProtozoaDB: dynamic visualization and exploration of protozoan genomes
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D547-D552; doi:10.1093/nar/gkm820 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Bindu Gajria, Amit Bahl, John Brestelli, Jennifer Dommer, Steve Fischer, Xin Gao, Mark Heiges, John Iodice, Jessica C. Kissinger, Aaron J. Mackey, Deborah F. Pinney, David S. Roos, Christian J. Stoeckert, Jr, Haiming Wang, and Brian P. Brunk

ToxoDB: an integrated Toxoplasma gondii database resource
Nucleic Acids Research Advance Access published on November 14, 2007
Nucl. Acids Res. 2008 36: D553-D556; doi:10.1093/nar/gkm981 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Tristan Rossignol, Pierre Lechat, Christina Cuomo, Qiandong Zeng, Ivan Moszer, and Christophe d’Enfert

CandidaDB: a multi-genome database for Candida species and related Saccharomycotina
Nucleic Acids Research Advance Access published on November 26, 2007
Nucl. Acids Res. 2008 36: D557-D561; doi:10.1093/nar/gkm1010 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jongsun Park, Bongsoo Park, Kyongyong Jung, Suwang Jang, Kwangyul Yu, Jaeyoung Choi, Sunghyung Kong, Jaejin Park, Seryun Kim, Hyojeong Kim, Soonok Kim, Jihyun F. Kim, Jaime E. Blair, Kwangwon Lee, Seogchan Kang, and Yong-Hwan Lee

CFGP: a web-based, comparative fungal genomics platform
Nucleic Acids Research Advance Access published on October 18, 2007
Nucl. Acids Res. 2008 36: D562-D571; doi:10.1093/nar/gkm758 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Rainer Winnenburg, Martin Urban, Andrew Beacham, Thomas K. Baldwin, Sabrina Holland, Magdalen Lindeberg, Hilde Hansen, Christopher Rawlings, Kim E. Hammond-Kosack, and Jacob Köhler

PHI-base update: additions to the pathogen–host interaction database
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D572-D576; doi:10.1093/nar/gkm858 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Eurie L. Hong, Rama Balakrishnan, Qing Dong, Karen R. Christie, Julie Park, Gail Binkley, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kathy K. Zhu, Kara Dolinski, David Botstein, and J. Michael Cherry

Gene Ontology annotations at SGD: new data sources and annotation methods
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2008 36: D577-D581; doi:10.1093/nar/gkm909 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Alexie Papanicolaou, Steffi Gebauer-Jung, Mark L. Blaxter, W. Owen McMillan, and Chris D. Jiggins

ButterflyBase: a platform for lepidopteran genomics
Nucleic Acids Research Advance Access published on October 12, 2007
Nucl. Acids Res. 2008 36: D582-D587; doi:10.1093/nar/gkm853 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Robert J. Wilson, Joshua L. Goodman, Victor B. Strelets, and The FlyBase Consortium

FlyBase: integration and improvements to query tools
Nucleic Acids Research Advance Access published on December 26, 2007
Nucl. Acids Res. 2008 36: D588-D593; doi:10.1093/nar/gkm930 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Marc S. Halfon, Steven M. Gallo, and Casey M. Bergman

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
Nucleic Acids Research Advance Access published on November 26, 2007
Nucl. Acids Res. 2008 36: D594-D598; doi:10.1093/nar/gkm876 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Sofia M.C. Robb, Eric Ross, and Alejandro Sánchez Alvarado

SmedGD: the Schmidtea mediterranea genome database
Nucleic Acids Research Advance Access published on September 18, 2007
Nucl. Acids Res. 2008 36: D599-D606; doi:10.1093/nar/gkm684 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract James C. Sullivan, Adam M. Reitzel, and John R. Finnerty

Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis
Nucleic Acids Research Advance Access published on November 3, 2007
Nucl. Acids Res. 2008 36: D607-D611; doi:10.1093/nar/gkm941 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Anthony Rogers, Igor Antoshechkin, Tamberlyn Bieri, Darin Blasiar, Carol Bastiani, Payan Canaran, Juancarlos Chan, Wen J. Chen, Paul Davis, Jolene Fernandes, Tristan J. Fiedler, Michael Han, Todd W. Harris, Ranjana Kishore, Raymond Lee, Sheldon McKay, Hans-Michael Müller, Cecilia Nakamura, Philip Ozersky, Andrei Petcherski, Gary Schindelman, Erich M. Schwarz, Will Spooner, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Karen Yook, Richard Durbin, Lincoln D. Stein, John Spieth, and Paul W. Sternberg

WormBase 2007
Nucleic Acids Research Advance Access published on November 8, 2007
Nucl. Acids Res. 2008 36: D612-D617; doi:10.1093/nar/gkm975 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Matthew Bashton, Irene Nobeli, and Janet M. Thornton

PROCOGNATE: a cognate ligand domain mapping for enzymes
Nucleic Acids Research Advance Access published on August 24, 2007
Nucl. Acids Res. 2008 36: D618-D622; doi:10.1093/nar/gkm611 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ron Caspi, Hartmut Foerster, Carol A. Fulcher, Pallavi Kaipa, Markus Krummenacker, Mario Latendresse, Suzanne Paley, Seung Y. Rhee, Alexander G. Shearer, Christophe Tissier, Thomas C. Walk, Peifen Zhang, and Peter D. Karp

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
Nucleic Acids Research Advance Access published on October 27, 2007
Nucl. Acids Res. 2008 36: D623-D631; doi:10.1093/nar/gkm900 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Chong Su, Jose M. Peregrin-Alvarez, Gareth Butland, Sadhna Phanse, Vincent Fong, Andrew Emili, and John Parkinson

Bacteriome.org—an integrated protein interaction database for E. coli
Nucleic Acids Research Advance Access published on October 16, 2007
Nucl. Acids Res. 2008 36: D632-D636; doi:10.1093/nar/gkm807 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Michael Livstone, Rose Oughtred, Daniel H. Lackner, Jürg Bähler, Valerie Wood, Kara Dolinski, and Mike Tyers

The BioGRID Interaction Database: 2008 update
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D637-D640; doi:10.1093/nar/gkm1001 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Roberta Alfieri, Ivan Merelli, Ettore Mosca, and Luciano Milanesi

The cell cycle DB: a systems biology approach to cell cycle analysis
Nucleic Acids Research Advance Access published on December 26, 2007
Nucl. Acids Res. 2008 36: D641-D645; doi:10.1093/nar/gkm873 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou Doudieu, Volker Stümpflen, and H. Werner Mewes

CORUM: the comprehensive resource of mammalian protein complexes
Nucleic Acids Research Advance Access published on October 26, 2007
Nucl. Acids Res. 2008 36: D646-D650; doi:10.1093/nar/gkm936 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Philipp Pagel, Matthias Oesterheld, Oksana Tovstukhina, Norman Strack, Volker Stümpflen, and Dmitrij Frishman

DIMA 2.0—predicted and known domain interactions
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D651-D655; doi:10.1093/nar/gkm996 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, and Raja Jothi

DOMINE: a database of protein domain interactions
Nucleic Acids Research Advance Access published on October 2, 2007
Nucl. Acids Res. 2008 36: D656-D661; doi:10.1093/nar/gkm761 [Abstract] [FREE Full Text] [Print PDF][Screen PDF] [Supplementary Data]  

Get checked abstract Emre Guney, Nurcan Tuncbag, Ozlem Keskin, and Attila Gursoy

HotSprint: database of computational hot spots in protein interfaces
Nucleic Acids Research Advance Access published on October 24, 2007
Nucl. Acids Res. 2008 36: D662-D666; doi:10.1093/nar/gkm813 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Benoit H. Dessailly, Marc F. Lensink, Christine A. Orengo, and Shoshana J. Wodak

LigASite—a database of biologically relevant binding sites in proteins with known apo-structures
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D667-D673; doi:10.1093/nar/gkm839 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John Beaver, Peter Dresslar, Jason Nerothin, and Heather A. Carlson

Binding MOAD, a high-quality protein–ligand database
Nucleic Acids Research Advance Access published on November 30, 2007
Nucl. Acids Res. 2008 36: D674-D678; doi:10.1093/nar/gkm911 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Wuming Gong, Dihan Zhou, Yongliang Ren, Yejun Wang, Zhixiang Zuo, Yanping Shen, Feifei Xiao, Qi Zhu, Ailing Hong, Xiaochuan Zhou, Xiaolian Gao, and Tongbin Li

PepCyber:PPEP: a database of human protein–protein interactions mediated by phosphoprotein-binding domains
Nucleic Acids Research Advance Access published on December 26, 2007
Nucl. Acids Res. 2008 36: D679-D683; doi:10.1093/nar/gkm854 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl Jensen, and Peer Bork

STITCH: interaction networks of chemicals and proteins
Nucleic Acids Research Advance Access published on December 15, 2007
Nucl. Acids Res. 2008 36: D684-D688; doi:10.1093/nar/gkm795 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jürgen Dönitz, Björn Goemann, Muriel Lizé, Holger Michael, Nicole Sasse, Edgar Wingender, and Anatolij P. Potapov

EndoNet: an information resource about regulatory networks of cell-to-cell communication
Nucleic Acids Research Advance Access published on November 27, 2007
Nucl. Acids Res. 2008 36: D689-D694; doi:10.1093/nar/gkm940 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Rune Linding, Lars Juhl Jensen, Adrian Pasculescu, Marina Olhovsky, Karen Colwill, Peer Bork, Michael B. Yaffe, and Tony Pawson

NetworKIN: a resource for exploring cellular phosphorylation networks
Nucleic Acids Research Advance Access published on November 2, 2007
Nucl. Acids Res. 2008 36: D695-D699; doi:10.1093/nar/gkm902 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, and Shankar Subramaniam

The Molecule Pages database
Nucleic Acids Research Advance Access published on October 26, 2007
Nucl. Acids Res. 2008 36: D700-D706; doi:10.1093/nar/gkm907 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract P. Flicek, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, T. Eyre, S. Fitzgerald, J. Fernandez-Banet, S. Gräf, S. Haider, M. Hammond, R. Holland, K. L. Howe, K. Howe, N. Johnson, A. Jenkinson, A. Kähäri, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. J. Vilella, J. Vogel, S. White, M. Wood, E. Birney, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, T. J. P. Hubbard, A. Kasprzyk, G. Proctor, J. Smith, A. Ureta-Vidal, and S. Searle

Ensembl 2008
Nucleic Acids Research Advance Access published on November 13, 2007
Nucl. Acids Res. 2008 36: D707-D714; doi:10.1093/nar/gkm988 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ann-Marie Mallon, Andrew Blake, and John M. Hancock

EuroPhenome and EMPReSS: online mouse phenotyping resource
Nucleic Acids Research Advance Access published on September 28, 2007
Nucl. Acids Res. 2008 36: D715-D718; doi:10.1093/nar/gkm728 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Carl J. Schmidt, Michael Romanov, Oliver Ryder, Vincent Magrini, Matthew Hickenbotham, Jarret Glasscock, Sean McGrath, Elaine Mardis, and Lincoln D. Stein

Gallus GBrowse: a unified genomic database for the chicken
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D719-D723; doi:10.1093/nar/gkm783 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Judith A. Blake, and the Mouse Genome Database Group

The Mouse Genome Database (MGD): mouse biology and model systems
Nucleic Acids Research Advance Access published on December 23, 2007
Nucl. Acids Res. 2008 36: D724-D728; doi:10.1093/nar/gkm961 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Ling V. Sun, Ke Jin, Yiming Liu, Wenwei Yang, Xing Xie, Lin Ye, Li Wang, Lin Zhu, Sheng Ding, Yi Su, Jie Zhou, Min Han, Yuan Zhuang, Tian Xu, Xiaohui Wu, Ning Gu, and Yang Zhong

PBmice: an integrated database system of piggyBac (PB) insertional mutations and their characterizations in mice
Nucleic Acids Research Advance Access published on October 11, 2007
Nucl. Acids Res. 2008 36: D729-D734; doi:10.1093/nar/gkm790 [Abstract] [FREE Full Text] [Print PDF][Screen PDF]  

Get checked abstract Jue Ruan, Heng Li, Zhongzhong Chen, Avril Coghlan, Lachlan James M. Coin, Yiran Guo, Jean-Karim Hériché, Yafeng Hu, Karsten Kristiansen, Ruiqiang Li, Tao Liu, Alan Moses, Junjie Qin, Søren Vang, Albert J. Vilella, Abel Ureta-Vidal, Lars Bolund, Jun Wang, and Richard Durbin

TreeFam: 2008 Update
Nucleic Acids Research Advance Access published on December 1, 2007
Nucl. Acids Res. 2008 36: D735-D740; doi:10.1093/nar/gkm1005 [Abstract]