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Information retrieval and sliding window programs

Information retrieval and sliding window programs. April 5, 2011 Hand in Homework #1. Homework #2 due Tuesday, April 12. Learning objectives- Understand the general arrangement of biological data at NCBI. Be able to retrieve information on a particular subject in the literature.

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Information retrieval and sliding window programs

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  1. Information retrieval and sliding window programs • April 5, 2011 • Hand in Homework #1. • Homework #2 due Tuesday, April 12. • Learning objectives- • Understand the general arrangement of biological data at NCBI. • Be able to retrieve information on a particular subject in the literature. • Sliding window programs

  2. Primary public domain bioinformatics servers Public Domain Bioinformatics Facilities Genome Net (KEGG & DDBJ) Japan European Bioinformatics Institute (EBI) United Kingdom National Center For Biotechnology Information (NCBI) United States Databases Databases Analysis Tools Analysis Tools Databases Analysis Tools

  3. NCBI ENTREZ • A platform that provides access to and links to databases with biological information ENTREZ PubMed PopSet Genomes Protein databases OMIM Taxonomy GenBank MedLine

  4. NCBI ENTREZ MedLine Literature Database OMIM Database of human genes and genetic disorders GenBank Database of all publicly available DNA sequences Database of amino acid sequences from Uniprot, Protein Research Foundation, PDB. Protein databases Database of genomes from organisms and viruses Genomes Database of DNA sequences that have been collected to analyze the evolutionary relatedness of a population. PopSet Taxonomy Database of names of organisms with sequences in GenBank.

  5. Literature Databases • Medline/Pubmed • OMIM • CSULA Library • Bookshelf (from NCBI) • Melvyl (Books at UC Libraries) • Other molecular life science databases • Science Direct • Pub Med Central • Free Medical Journals • LinkOut Journals • Wiley InterScience

  6. Medline Database • Producer: National Library of Med • Database size: >15 million records • Publications Indexed: More than 5000 journals • Years Covered: 1966-present • Update Frequency: Daily • Papers in press are available

  7. OMIM-Online Mendelian Inheritance in Man • A catalog of human genes linked to diseases • Victor A. McKusick at Johns Hopkins University • A good place to start when you want to research a certain disease or biological molecule • This database is cross-referenced to PubMed and other NCBI-based databases

  8. Workshop#2

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