NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

Pruitt, Kim D.; Tatusova, Tatiana; Maglott, Donna

doi:10.1093/nar/gkl842

Cited by 3,326 publications

(2,393 citation statements)

References 15 publications

Supporting

Mentioning

2,320

Contrasting

Unclassified

Order By: Relevance

“…Then, we used dbSNP rsIDs for each nSNP (http://www.ncbi.nlm. nih.gov/projects/SNP/) to generate a RefSeq identifier (Pruitt et al 2007). This information was used to map each nSNP onto the 44-species protein alignments available in the UCSC Genome Browser (Kuhn et al 2009).…”

Section: Methodsmentioning

confidence: 99%

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations

et al. 2009

View full text Add to dashboard Cite

As the cost of DNA sequencing drops, we are moving beyond one genome per species to one genome per individual to improve prevention, diagnosis, and treatment of disease by using personal genotypes. Computational methods are frequently applied to predict impairment of gene function by nonsynonymous mutations in individual genomes and single nucleotide polymorphisms (nSNPs) in populations. These computational tools are, however, known to fail 15%-40% of the time. We find that accurate discrimination between benign and deleterious mutations is strongly influenced by the long-term (among species) history of positions that harbor those mutations. Successful prediction of known diseaseassociated mutations (DAMs) is much higher for evolutionarily conserved positions and for original-mutant amino acid pairs that are rarely seen among species. Prediction accuracies for nSNPs show opposite patterns, forecasting impediments to building diagnostic tools aiming to simultaneously reduce both false-positive and false-negative errors. The relative allele frequencies of mutations diagnosed as benign and damaging are predicted by positional evolutionary rates. These allele frequencies are modulated by the relative preponderance of the mutant allele in the set of amino acids found at homologous sites in other species (evolutionarily permissible alleles [EPAs]). The nSNPs found in EPAs are biochemically less severe than those missing from EPAs across all allele frequency categories. Therefore, it is important to consider position evolutionary rates and EPAs when interpreting the consequences and population frequencies of human mutations. The impending sequencing of thousands of human and many more vertebrate genomes will lead to more accurate classifiers needed in real-world applications.

show abstract

Section: Methodsmentioning

confidence: 99%

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations

et al. 2009

View full text Add to dashboard Cite

show abstract

“…The genomic, mRNA and protein sequences were retrieved from the NCBI RefSeq (www.ncbi.nlm.nih.gov/projects/RefSeq) collection [Pruitt et al, 2007] and they are accessible for downloading in FASTA (text-based) format, while the variant records are downloadable in Excel (Microsoft, Redmond, WA) format. The short descriptions of diseases are organized according to their association with intermediate filament type and links are included to the respective protein information page, to references in the HIFD, as well to the Online Mendelian Inheritance in Man (OMIM) database.…”

Section: Database Content and Organizationmentioning

confidence: 99%

The Human Intermediate Filament Database: comprehensive information on a gene family involved in many human diseases

et al. 2008

View full text Add to dashboard Cite

Communicated by A. Jamie CuticchiaWe describe a revised and expanded database on human intermediate filament proteins, a major component of the eukaryotic cytoskeleton. The family of 70 intermediate filament genes (including those encoding keratins, desmins, and lamins) is now known to be associated with a wide range of diverse diseases, at least 72 distinct human pathologies, including skin blistering, muscular dystrophy, cardiomyopathy, premature aging syndromes, neurodegenerative disorders, and cataract. To date, the database catalogs 1,274 manually-curated pathogenic sequence variants and 170 allelic variants in intermediate filament genes from over 459 peer-reviewed research articles. Unrelated cases were collected from all of the six sequence homology groups and the sequence variations were described at cDNA and protein levels with links to the related diseases and reference articles. The mutations and polymorphisms are presented in parallel with data on protein structure, gene, and chromosomal location and basic information on associated diseases. Detailed statistics relating to the variants records in the database are displayed by homology group, mutation type, affected domain, associated diseases, and nucleic and amino acid substitutions. Multiple sequence alignment algorithms can be run from queries to determine DNA or protein sequence conservation. Literature sources can be interrogated within the database and external links are provided to public databases. The database is freely and publicly accessible online at www.interfil.org (last accessed 13 September 2007). Users can query the database by various keywords and the search results can be downloaded. It is anticipated that the Human Intermediate Filament Database (HIFD) will provide a useful resource to study human genome variations for basic scientists, clinicians, and students alike. Hum Mutat 29(3), [351][352][353][354][355][356][357][358][359][360] 2008.

show abstract

“…Using the full-length sequences of S. cerevisiae Opy2p and Ste50p, we assembled a set of 30 Opy2p-like protein sequences and a set of 28 Ste50p-like protein sequences from fungal species by performing PSI-Blast searches (Altschul et al, 1997) against the NCBI RefSeq database (Pruitt et al, 2007). Multiple sequence alignments within each set were derived with the L-INS-i iterative refinement method of the MAFFT 6 program (Katoh and Toh, 2008), and analyzed with Jalview 2.4 (Waterhouse et al, 2009).…”

Section: Bioinformatic Analysis Of Ste50p-ra Domain and The Fid Regiomentioning

confidence: 99%

Binding the Atypical RA Domain of Ste50p to the Unfolded Opy2p Cytoplasmic Tail Is Essential for the High-Osmolarity Glycerol Pathway

Ekiel

Sulea

Jansen³

et al. 2009

MBoC

View full text Add to dashboard Cite

show abstract

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

Cited by 3,326 publications

References 15 publications

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations

The Human Intermediate Filament Database: comprehensive information on a gene family involved in many human diseases

Binding the Atypical RA Domain of Ste50p to the Unfolded Opy2p Cytoplasmic Tail Is Essential for the High-Osmolarity Glycerol Pathway

Contact Info

Product

Resources

About