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Sequence Databases: : Database Directories and Lists

Sequence Databases: : Database Directories and Lists. Nucleic Acids Research : Annual Database Issue http://www.nar.oupjournals.org/content/vol31/issue1/ Description of molecular biology and bioinformatics databases

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Sequence Databases: : Database Directories and Lists

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  1. Sequence Databases: :Database Directories and Lists • Nucleic Acids Research: Annual Database Issuehttp://www.nar.oupjournals.org/content/vol31/issue1/ • Description of molecular biology and bioinformatics databases • Introduction to Molecular Biology Databaseshttp://www.ebi.ac.uk/swissprot/Publications/mbd1.html • Good starting place for novices

  2. Primary Sequence Databases • International Nucleotide Sequence Database Collaboration http://www.ncbi.nlm.nih.gov/collab/ DNA sequences and derived protein sequences • GenBank,NCBI http://www.ncbi.nlm.nih.gov • European Molecular Biology Laboratory, EMBL http://www.embl.org/ • DNA Data Bank of Japan, DDBJ http://www.ddbj.nig.ac.jp/ • Other • Protein Data Bank - three-dimensional structures of protein

  3. Protein Data Bank: http://www.rcsb.org • 3-dimensional structure of proteins • 1971, BNL (Brookhaven NationalLaboratories) • archive for biologicalmacromolecular crystal structures • 1980s • increase in the number of deposited structures. • 1998, RCSB(Research Collaboratory for Structural Bioinformatics) • NSF, DOE, and two units of NIH:NIGMS National Institute Of General Medical Sciences and NLM National Library Of Medicine.

  4. Secondary Sequence Databases: SWISS-PROT/TrEMBL • http://www.expasy.ch/ • Annotated protein sequences, • 1986, developed by the SWISS-PROT groups at SIB and European Bioinformatics Institute. • 1987, maintained collaboratively by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library (EBI). • cross-referenced to several other databases, EMBL, PROSITE pattern database and PDB."

  5. Secondary Sequence Databases:Protein Identification Resource (PIR) • International Protein Sequence Database http://pir.georgetown.edu/ • 1988, Georgetown University Medical Center, Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID) • "a comprehensive, non-redundant, expertly annotated, fully classified and extensively cross-referenced protein sequence database in the public domain"

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