Database resources of the National Center for Biotechnology Information

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

doi:10.1093/nar/gkm1000

Cited by 864 publications

(665 citation statements)

References 38 publications

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“…The majority of the nucleotide and protein sequence data set used in study were retrieved from National Center for Biotechnology Information (NCBI) (Wheeler et al 2007) and some of them were retrieved from the RNA virus database (http://tree.bio.ed.ac.uk/rnavirusdb/). The complete genome sequences of MBFVs were collected from viral genomes resource (NCBI) (www.ncbi.nlm.nih.gov/ genomes/VIRUSES/viruses.html; Bao et al 2004) in GenBank format (Benson et al 2010) using RefSeq data ).…”

Section: Sequence Datasets Informationmentioning

confidence: 99%

Molecular-based identification and phylogeny of genomic and proteomic sequences of mosquito-borne flavivirus

et al. 2013

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Mosquito-borne flaviviruses (MBFVs) are important cause of emerging and re-emerging human diseases nearly worldwide, transmitted by arthropod vectors (mostly aedes and culex mosquitoes), with particular reference to yellow fever virus, Japanese encephalitis virus, dengue fever virus, St. Louis encephalitis virus, Murray Valley encephalitis virus, etc. In over 100 countries, more than 2.5 billion people are at risk of infection, and approximately 20 million infections are reported annually. Through the analysis of gene sequence data of these virus populations it is possible to infer phylogenetic relationships, which in turn can yield important epidemiological information, including their demographic history. Early attempts to define the evolutionary relationships and origins of viruses in the genus flavivirus are hampered by the lack of genetic information particularly amongst the MBFVs. In this study, complete genome, translated polyprotein, structural and non-structural proteins of MBFVs have been targeted and revealed an extensive series of clades defined by their epidemiology and disease associations. The branching patterns of at the deeper nodes of the resultant trees were different from those reported in the previous study. The significance of these observations is discussed.

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Section: Sequence Datasets Informationmentioning

confidence: 99%

Molecular-based identification and phylogeny of genomic and proteomic sequences of mosquito-borne flavivirus

et al. 2013

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“…For each SNP the table contains the dbSNP identifier [Wheeler et al, 2008], its position on the genome, the alternative allele, and the frequency of the SNP in 11 different populations. For each population the frequency is depicted in a pie chart, where the blue part represents the percentage of the allele found in the reference genome, whereas orange stands for the percentage of the alternative allele.…”

Section: Gene Searchmentioning

confidence: 99%

The Roche Cancer Genome Database (RCGDB)

et al. 2010

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Sequence variations are being studied for a better understanding of the mechanism and development of cancer as a mutation-driven disease. The systematic sequencing of genes in tumors and technological advances in high-throughput techniques combined with efficient data acquisition methods have resulted in an explosion of available cancer genome-related data. Despite the technological progress and increase of data, improvements in the application area, for example, drug target discovery, have failed to keep pace with increased research and development spending. One reason for this discrepancy is the ever increasing number of databases and the absence of a unified access to the mutation data. Currently, researchers typically have to browse several, often highly specialized databases to obtain the required information. A more complete understanding of relations and dependencies between mutations and cancer, however, requires the availability of an efficient integrative cancer genome information system. To facilitate this, we developed the Roche Cancer Genome Database (RCGDB), a freely available biological information system integrating different kinds of mutation data. The database is the first comprehensive integration of disparate cancer genome data like single nucleotide variants, single nucleotide polymorphisms, and chromosomal aberrations (CGH and FISH). RCGDB is freely accessible via a Google-like Web interface at

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“…Different inputs of selected homologues and their alignment were used: 61 unaligned sequences from BLink [Wheeler et al, 2004], SIFT aligns, remove 100% identical; ClustalX [Jeanmougin et al, 1998] alignment of 61 sequences from BLink, remove 100% identical; Query sequence, SIFT finds homologues and aligns, remove 100% identical. Scores <0.05 are predicted to affect protein function, scores ≥ 0.05 are predicted to be tolerated (Table 2).…”

Section: In Silico Analysesmentioning

confidence: 99%

“…5 A negative family history indicates that no first degree relatives were reported with dementia or FTD. 6 SIFT consensus predictions [Ng and Henikoff, 2003]: A) 61 unaligned sequences from BLink [Wheeler et al, 2004], SIFT aligns, remove 100% identical. B) ClustalX [Jeanmougin et al, 1998] alignment of 61 sequences from BLink, remove 100% identical.…”

Section: In Silico Analysesmentioning

confidence: 99%

Mutations other than null mutations producing a pathogenic loss of progranulin in frontotemporal dementia

et al. 2007

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Null mutations in the progranulin gene (GRN, PGRN) were recently identified as the causal mechanism underlying frontotemporal dementia (FTD) with ubiquitin-positive brain pathology linked to chromosome 17 (FTDU-17). In a Belgian and French FTD series comprising 332 patients, we reported 13 PGRN null mutations which were mainly nonsense and frameshift mutations resulting in premature stop codons. Here we report in the same patient series three missense mutations of which two (c.743C>T, p.Pro248Leu and c.1294C>T, p.Arg432Cys) were predicted in silico to severely affect protein folding and/or processing leading to PGRN protein haploinsufficiency. In addition, we observed three sequence variations in the 5' regulatory region that might potentially affect PGRN transcription activity. Our findings extend the mutation spectrum in PGRN leading to loss of functional PGRN as the basis for FTD.

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Database resources of the National Center for Biotechnology Information

Cited by 864 publications

References 38 publications

Molecular-based identification and phylogeny of genomic and proteomic sequences of mosquito-borne flavivirus

Molecular-based identification and phylogeny of genomic and proteomic sequences of mosquito-borne flavivirus

The Roche Cancer Genome Database (RCGDB)

Mutations other than null mutations producing a pathogenic loss of progranulin in frontotemporal dementia

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