Interesting databases in the 2010 NAR issue

NAR 2010 databases

• Daniel Glez-Peña, Daniel Gómez-Blanco, Miguel Reboiro-Jato, Florentino Fdez-Riverola, and David Posada

            ALTER: program-oriented conversion of DNA and protein alignments

          Nucl. Acids Res. (2010) 38(suppl 2): W14-W18 doi:10.1093/nar/gkq321

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• Alexey V. Antonov, Esther E. Schmidt, Sabine Dietmann, Maria Krestyaninova, and Henning Hermjakob

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases

          Nucl. Acids Res. (2010) 38(suppl 2): W78-W83 doi:10.1093/nar/gkq482

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• Kunlin Zhang, Sijia Cui, Suhua Chang, Liuyan Zhang, and Jing Wang

i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study

Nucl. Acids Res. (2010) 38(suppl 2): W90-W95 doi:10.1093/nar/gkq324

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• Vivek Kaimal, Eric E. Bardes, Scott C. Tabar, Anil G. Jegga, and Bruce J. Aronow

ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

Nucl. Acids Res. (2010) 38(suppl 2): W96-W102 doi:10.1093/nar/gkq418

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• Jignesh R. Parikh, Bertram Klinger, Yu Xia, Jarrod A. Marto, and Nils Blüthgen

Discovering causal signaling pathways through gene-expression patterns

Nucl. Acids Res. (2010) 38(suppl 2): W109-W117 doi:10.1093/nar/gkq424

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• Y.-T. Wang, Y.-H. Huang, Y.-C. Chen, C.-L. Hsu, and U.-C. Yang

PINT: Pathways INtegration Tool

Nucl. Acids Res. (2010) 38(suppl 2): W124-W131 doi:10.1093/nar/gkq499

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• Ludovic Cottret, David Wildridge, Florence Vinson, Michael P. Barrett, Hubert Charles, Marie-France Sagot, and Fabien Jourdan

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

Nucl. Acids Res. (2010) 38(suppl 2): W132-W137 doi:10.1093/nar/gkq312

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• Marija Cvijovic, Roberto Olivares-Hernández, Rasmus Agren, Niklas Dahr, Wanwipa Vongsangnak, Intawat Nookaew, Kiran Raosaheb Patil, and Jens Nielsen

BioMet Toolbox: genome-wide analysis of metabolism

Nucl. Acids Res. (2010) 38(suppl 2): W144-W149 doi:10.1093/nar/gkq404

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• Richard Côté, Florian Reisinger, Lennart Martens, Harald Barsnes, Juan Antonio Vizcaino, and Henning Hermjakob

The Ontology Lookup Service: bigger and better

Nucl. Acids Res. (2010) 38(suppl 2): W155-W160 doi:10.1093/nar/gkq331

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• Xin He, Yanen Li, Radhika Khetani, Barry Sanders, Yue Lu, Xu Ling, ChengXiang Zhai, and Bruce Schatz

BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects

Nucl. Acids Res. (2010) 38(suppl 2): W175-W181 doi:10.1093/nar/gkq544

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• Scott F. Saccone, Raphael Bolze, Prasanth Thomas, Jiaxi Quan, Gaurang Mehta, Ewa Deelman, Jay A. Tischfield, and John P. Rice

SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study

Nucl. Acids Res. (2010) 38(suppl 2): W201-W209 doi:10.1093/nar/gkq513

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• Ignacio Medina, José Carbonell, Luis Pulido, Sara C. Madeira, Stefan Goetz, Ana Conesa, Joaquín Tárraga, Alberto Pascual-Montano, Ruben Nogales-Cadenas, Javier Santoyo, Francisco García, Martina Marbà, David Montaner, and Joaquín Dopazo

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling

Nucl. Acids Res. (2010) 38(suppl 2): W210-W213 doi:10.1093/nar/gkq388

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• Miguel Vazquez, Ruben Nogales-Cadenas, Javier Arroyo, Pedro Botías, Raul García, Jose M. Carazo, Francisco Tirado, Alberto Pascual-Montano, and Pedro Carmona-Saez

MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures

Nucl. Acids Res. (2010) 38(suppl 2): W228-W232 doi:10.1093/nar/gkq476

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• Maria José Nueda, José Carbonell, Ignacio Medina, Joaquín Dopazo, and Ana Conesa

Serial Expression Analysis: a web tool for the analysis of serial gene expression data

Nucl. Acids Res. (2010) 38(suppl 2): W239-W245 doi:10.1093/nar/gkq488

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• Haim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, and Nir Ben-Tal

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids

Nucl. Acids Res. (2010) 38(suppl 2): W529-W533 doi:10.1093/nar/gkq399

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• Gilad Wainreb, Haim Ashkenazy, Yana Bromberg, Alina Starovolsky-Shitrit, Turkan Haliloglu, Eytan Ruppin, Karen B. Avraham, Burkhard Rost, and Nir Ben-Tal

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data

Nucl. Acids Res. (2010) 38(suppl 2): W523-W528 doi:10.1093/nar/gkq528

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• Jiten Bhagat, Franck Tanoh, Eric Nzuobontane, Thomas Laurent, Jerzy Orlowski, Marco Roos, Katy Wolstencroft, Sergejs Aleksejevs, Robert Stevens, Steve Pettifer, Rodrigo Lopez, and Carole A. Goble

BioCatalogue: a universal catalogue of web services for the life sciences

Nucl. Acids Res. (2010) 38(suppl 2): W689-W694 doi:10.1093/nar/gkq394

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• Mickael Goujon, Hamish McWilliam, Weizhong Li, Franck Valentin, Silvano Squizzato, Juri Paern, and Rodrigo Lopez

A new bioinformatics analysis tools framework at EMBL–EBI

Nucl. Acids Res. (2010) 38(suppl 2): W695-W699 doi:10.1093/nar/gkq313

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• Huabin Hou, Fangqing Zhao, LingLin Zhou, Erle Zhu, Huajing Teng, Xiaokun Li, Qiyu Bao, Jinyu Wu, and Zhongsheng Sun

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

Nucl. Acids Res. (2010) 38(suppl 2): W732-W736 doi:10.1093/nar/gkq302

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• Dougu Nam, Jin Kim, Seon-Young Kim, and Sangsoo Kim

GSA-SNP: a general approach for gene set analysis of polymorphisms

Nucl. Acids Res. (2010) 38(suppl 2): W749-W754 doi:10.1093/nar/gkq428

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• Zefeng Zhang, Hao Lin, and Bin Ma

ZOOM Lite: next-generation sequencing data mapping and visualization software

Nucl. Acids Res. (2010) 38(suppl 2): W743-W748 doi:10.1093/nar/gkq538

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