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NCBI: something old, something new What is NCBI? On November 4, 1988 that President Ronald Reagan signed the Health Omnibus Extension Act to create The National Center for Biotechnology Information as part of National Library of Medicine at NIH. • Create automated systems for knowledge about molecular biology, biochemistry, and genetics. • Perform research into advanced methods of analyzing and interpreting molecular biology data. • Enable biotechnology researchers and medical care personnel to use the systems and methods developed. The National Center for Biotechnology Information (NCBI) Bethesda,MD Part of National Library of Medicine (NLM) at National Institutes of Health (NIH) NCBI: down on the farm • Genome assembly and annotation • Pre-computed relationships for: – – – – – – – Protein clusters “Nearby” nucleic acid EST unigene clusters Putative homologous genes Conserved protein domains SNPs Reciprocal links NCBI Daily Users 3,000,000 2,500,000 Web page views: 26 million per day Web users: 2.7 million per day 2,000,000 Data downloaded: 23 TB per day Peak web hits: 7,000 per second 1,500,000 1,000,000 500,000 0 1 9 9 7 1 9 9 8 1 9 9 9 2 0 0 0 2 0 0 1 2 0 0 2 2 0 0 3 2 0 0 4 2 0 0 5 2 0 0 6 2 0 0 7 2 0 0 8 2 0 0 9 2 0 1 0 2 0 1 1 NCBI: Integrated platform for data analysis and visualization Primary Data sets: BioProject, BioSample, Genome, Assembly, Annotation Curated data sets: Refseq genomes, Gene, Protein Clusters, Pathogenic Factors, Targeted Loci Entrez search and retrieval system Analysis Tools: Annotation pipeline, genome alignments, protein clustering, multiple alignments, (assembly, SNP) Validation Tools: assembly and annotation quality assesment Visualization Tools: genomeMap, distance tree, proteinMap, Genome Comparison How to navigate through NCBI resources Text search in Entrez Search in MapViewer All databases Specialized databases Use limits page Sequence search BLAST Genome BLAST Splign/ProSplign Marker/gene name Accession # Organism name Pre-computed similarities Blink CDD TaxPlot Use Genome specific resources Getting Started: NCBI Home Page Search resources by name http://www.ncbi.nlm.nih.gov Search All Databases in Entrez Learn more: Newsletter Education mailing lists NCBI Resources by name How to: NCBI help pages The NCBI Handbook Keeping up with what’s new NCBI News on Bookshelf www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=newsncbi Genetic Testing Registry (GTR) BLAST Entrez Assembly Entrez Genome redesign Microbial Genome Resources NCBI on Facebook and Twitter David Lipman on GenBank 25th Anniversary