Ncbi reference sequence (refseq): a curated non - redundant sequence database of genomes

By Kim D. Pruitt, Tatiana A. Tatusova, Donna R. Maglott. 2005

1,160 citations recorded by the source corpus.

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Citations in the corpus

The UCSC Genome Browser Database: update 2006 (2005, background): “Other areas of improvement are inclusion of RefSeq (13) mRNAs as initial candidates, pairing of proteins and mRNAs, coverage of splice isoforms, weighting of RefSeq and Mammalian Gene Collection (MGC) (14) genes and iden-tiﬁcation of coding DNA sequence (CDS) regions within mRNA sequences.”
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens (2008, background): “The ‘Gene’ tab contains general information extracted from NCBI Entrez Gene database including aliases, mRNA RefSeq accession numbers (5), gene structure, chromosomal localization, exon-intron structure, RefSeq splicing variants as well as links to the genome browsers MapViewer (6), UCSC Genome Brow”
The UCSC Genome Browser database: update 2010 (2009, background): “The tool is available via the Table Browser and from the details pages of the UCSC Genes and RefSeq Genes tracks.”
Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. (2006, methodology): “As the database was compiled using EST sequences, we blasted all exons against RefSeq (Pruitt et al., 2005) to find the”
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences (2015, methodology): “To generate an evolutionary sequence profile we used PSI-Blast with default parameters, querying a non-redundant protein database [25,47].”
Global topological features of cancer proteins in the human interactome (2006, methodology): “BLAST searches were run for the human genome as documented in version 9 of the Reference Sequence Database (Pruitt et al., 2005) against all proteins in the DIP (Salwinski et al., 2004) and MIPS Mammalian Protein-Protein Interaction databases (Pagel et al., 2005).”
Assessing the Evolutionary Impact of Amino Acid Mutations in the Human Genome (2008, background): “These potential gene regions were included in our analysis if they could be uniquely mapped to hg18 in a region containing a refseq18 gene [41].”
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes (2005, background): “In the future, because of the complexity of the CMR database and its omission of RNA-coding genes, other databases such as COGENT (29) and RefSeq (32) will have to be considered.”
Direct multiplexed measurement of gene expression with color-coded probe pairs (2008, unknown): “NM_006420 ARFGEF2 215931_s_at Hs00197455_m1 77 (2) 29 (1) D/D 42 (5) 47 (6) U/U 26.”
Reorganizing the protein space at the Universal Protein Resource (UniProt) (2011, methodology): “Currently, UniProt has defined 455 reference proteomes in close collaboration with Ensembl and NCBI Reference Sequence collection (RefSeq) (6).”
Choosing BLAST options for better detection of orthologs as reciprocal best hits (2008, methodology): “We used the 587 prokaryotic genomes available at the RefSeq database (Maglott et al., 2000; Pruitt et al., 2005 We ran NCBI's BLASTP comparisons of all the proteins encoded by the annotated genes of E.coli K12 against all the proteins encoded by the genes annotated in any other genome, and vice…”
ENCODE whole-genome data in the UCSC Genome Browser: update 2012 (2011, methodology): “Details pages for the annotated elements show evidence used to build the annotation such as UniProt (13), CCDS (14), RefSeq (15) and GenBank (16) sequences, and PubMed IDs for published experimental evidence.”
The UCSC Genome Browser Database: 2008 update (2007, methodology): “Compared to RefSeq, this gene set generally has about 10% more protein-coding genes, approximately five times as many putative non-coding genes, and about twice as many splice variants.”
Human protein reference database—2006 update (2005, background): “HPRD can be queried through gene symbols or a variety of database accession numbers such as RefSeq (10), OMIM (11), Swiss-Prot (12), HPRD and Entrez Gene (13).”
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, background): “Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.”