[医药卫生]3 Entrez-1.ppt

NCBI Molecular Biology Resources—— Entrez 王禄山 NCBI Resources About NCBI NCBI Sequence Databases Primary Database – GenBank Derivative Databases - RefSeq Entrez Databases and Text Searching BLAST The National Institutes of Health The National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) Created as a part of the National Library of Medicine in 1988 Establish public databases Research in computational biology Develop software tools for sequence analysis Disseminate biomedical information Tools: Entrez (1992) ，BLAST(1990), GenBank (1992) Free MEDLINE (PubMed, 1997) Other databases: dbEST, dbGSS, dbSTS, MMDB, OMIM, UniGene, GeneMap, Taxonomy, CGAP, SAGE, LocusLink, RefSeq NCBI WWW Users per Day Number of Users and Hits Per Day Home accessing the data Entrez Nucleotide Primary Data GenBank / DDBJ / EMBL 46,974,918 (98.86 %) Derivative Data RefSeq 533,236 (1.12 %) PDB (structures) 5,484 Third Party Annotation (TPA) 4,516 “Total” 47,518,338 GenBank: NCBI’s Primary Sequence Database Molecular Databases Primary Databases Original submissions by experimentalists Database staff organize but don’t add additional information Example: GenBank Derivative Databases Human curated compilation and correction of data Example: SWISS-PROT, NCBI RefSeq mRNA Computationally Derived Example: UniGene Combinations Example: NCBI Genome Assembly Primary vs. Derivative Databases The GenBank Record GenBank Records A Typical GenBank Record GenBank Record: Feature Table GenBank Record: Feature Table GenBank Record: sequence NCBI Homepage NCBI Homepage Online Help Using Entrez An integrated database search and retrieval system Entrez: Neighboring and Hard Links Database Searching with Entrez Using limits and field restriction to find mouse GAPD Linking and neighboring with mouse GAPD Entrez Nucleoti