Database resources of the National Center for Biotechnology

By David L. Wheeler, D. Church, S. Federhen, A. Lash, Thomas L. Madden, J. Pontius, G. Schuler, L. Schriml, Edwin Sequeira, Tatiana A. Tatusova and 1 more. Nucleic Acids Res., 2003

1,259 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ab99f2afd0f09ee707540022f0895a09fa1107f1

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Citations in the corpus

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. (2003, background): “Various efforts currently exist to assemble the expressed sequence populations into a unique index of genes, including the Gene Indices at The Institute for Genomic Research (TIGR) (6), Unigene at the National Center for Biotechnology Information (NCBI) (7), and STACKdb at the South African National”
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms (2004, methodology): “Each protein sequence in SGD is used as a query for the PSI-BLAST (Position-Speciﬁc Iterated BLAST) program (4) against the most recent version of the non-redundant (nr) protein sequence data set (5) at NCBI (6).”
EDGAR: A software framework for the comparative analysis of prokaryotic genomes (2009, background): “Various more sophisticated orthology identification approaches have been developed in the past, e.g. Clusters of Orthologous Genes (COG), InParanoid, OrthoMCL, Ensembl Compara, Homolo-gene, RoundUp, EggNOG, or OMA [17-24].”
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data (2005, methodology): “The prevailing 5 method for associating the latest gene identity and function annotations to probe sets on GeneChips is to map the Affymetrix ‘Representative Public ID’ for each probe set to the current version of gene and annotation databases such as UniGene ( 11 ,12), LocusLink/Entrez Gene (11,12)”
Histone modification levels are predictive for gene expression (2010, methodology): “To exclude the possibility that some of the RefSeq genes used in our analysis correspond to alternative transcripts of the same gene, all RefSeq genes were mapped to corresponding Unigene clusters (30), and only one RefSeq gene per cluster was kept, leaving 14,802 RefSeq genes for further analysis (”
GMAP: a genomic mapping and alignment program for mRNA and EST sequence (2005, background): “When multithreading is enabled, one thread handles reading of the input, one handles writing of the output alignments, and one or more worker threads each processes an individual cDNA sequence.”
Promoter features related to tissue specificity as measured by Shannon entropy (2005, background): “…to identify commonalities and differences in their promoters with the available complete genome sequences [16], libraries enriched for full-length cDNAs [17-19] and genome-wide surveys of gene expression using microarrays [14,20-24], SAGE [25], mRNAs [18] and expressed sequence tags (ESTs) [26].”
Gene structure and organization of the human β‐secretase (BACE) promoter (2004, methodology): “To amplify the human BACE 5′ flanking DNA, we performed a basi c local alignment search tool (BLAST) (13) search of the high-throughput geno me sequencing (HTGS) database against the 5 ′ end of BACE cDNA (GenBank accession number BC 036084) (14).”
GenBank: update (2004, background): “BLAST is discussed in more detail in a separate article in this issue (4).”
Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach (2003, background): “The NCBI Taxonomy (Wheeler et al. 2003), although declared as ‘‘not a phylogenetic or taxonomic authority,’’ agrees with the latest edition of Bergey’s Manual for most of the species studied in this work.”
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”
SVM-Prot: web-based support vector machine software for functional classification of a protein from its primary sequence (2003, background): “These include 46 families of enzymes from BRENDA (20), G-protein coupled receptors from GPCRDB (21), nuclear receptors from NucleaRDB (21), tyrosine receptor kinases derived from NCBI (31), five families of channels and one family of transporters from TCDB (22) and LGICdb (23) and DNA- and RNA-bindi”
Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets (2008, background): “…as I.M.A.G.E. CloneID, Affymetrix ID, or GenBank accession numbers to a gene-level identifier such as UniGene, RefSeq, or Entrez Gene ID. UniGene [69], which is an experimental system for automatically partitioning sequences into non-redundant gene-oriented clusters, is a popular choice to unify…”