Information retrieval and sliding window programs April 5, 2011 Hand in Homework #1. Homework #2 due Tuesday, April 12. Learning objectives- Understand.

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Presentation transcript:

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

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

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

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

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

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

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

Workshop#2