RefSeq and LocusLink: NCBI gene-centered resources

By Kim D. Pruitt, Donna R. Maglott. Nucleic Acids Res., 2001

935 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/f1933f8ae71ad3117338a6430e8c1c0eb5b88d96

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In Molecular Biology

Citations in the corpus

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine (2005, methodology): “The CDS sequences are extracted according to the UCSC refGene annotation tables [25,26].”
The Protein Information Resource (2003, neutral): “Direct entry report retrieval is based on sequence unique identiﬁers of all underlying databases, such as PIR, SWISS-PROT, or RefSeq.”
High-resolution protein complexes from integrating genomic information with molecular simulation (2009, background): “As a first step, as many as possible bacterial genomes (31) were scanned with the Pfam Hidden Markov Models (32) for the protein domain families HisKA (PF00512, describing the most abundant class of bacterial SK that this work exclusively concentrates on) and RR (PF00072).”
An automated method for finding molecular complexes in large protein interaction networks (2003, positive): “A BIND yeast import utility was developed to integrate data from SGD [12], RefSeq [44], Gene Registry http://genome-www.stanford.edu/ Saccharomyces/registry.html, the list of essential genes from the yeast deletion consortium [11] and GO terms [43].”
Features of protein-protein interactions in two-component signaling deduced from genomic libraries. (2007, methodology): “For this study, we queried the refseq database release 19 ( Pruitt and Maglott, 2001 ), which contains the sequences from 300 complete bacterial genomes.”
Identification of direct residue contacts in protein–protein interaction by message passing (2009, methodology): “ets, including mRNA and protein profiles, and neuronal spike activities. Material and Methods Database construction Domains were aligned and culled from the non-redundant refseq database (release 19) (38) using HMMER (39). Only genomic data from unique species were included to avoid over-sampling of”
GenePaint.org: an atlas of gene expression patterns in the mouse embryo (2004, methodology): “GenePaint.org uses the nomenclature for genes defined in LocusLink ( 11 ) and the Mouse Genome Database (12), which follow the rules set forth by the International Committee on Standardized Genetic Nomenclature for Mice (13).”
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004, positive): “In order to evaluate the H-Inv dataset, we compared all of the mapped H-Inv cDNAs with the Reference Sequence Collection (RefSeq) mRNA database (Pruitt and Maglott 2001) (Figure 2).”
NetAffx: Affymetrix probesets and annotations (2003, methodology): “These include annotations available in UniGene (1), GenBank, LocusLink (2), model organism databases, SWISS-PROT (3), OMIM, etc.”
Human Gene Mutation Database (HGMD®): 2003 update (2003, background): “…[www.gene.ucl.ac.uk/ nomenclature/; Povey et al., 2001], GeneCards [http://bioinformatics.weizmann.ac.il/cards; Rebhan et al., 1998], GeneClinics [www.geneclinics.org/; Pagon et al., 2002], and LocusLink [www.ncbi.nlm.nih.gov/LocusLink/; Pruitt and Maglott, 2001] have also been established.”