Biological databases

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Course work on biological databases

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Biological databases

  1. 1. Sucheta Tripathy7th October 2012
  2. 2.  Introduction. History of Genome Sequencing. Rationale behind genome sequencing. How genomes are sequenced. What happens next. ◦ Assembly and Annotation. ◦ Sequence Submissions. Microbial Genome Sequencing. Human Genome Project. ◦ Encode Project. ◦ 1000 genomes project.
  3. 3.  Write a paragraph (less than 1000 characters) on “why you think more genomes need to be sequenced OR not sequenced”. tsucheta@iicb.res.in/tsucheta@gmail.com
  4. 4.  Literature search databases. NA and protein databases. Animal and plant databases Ensembl Genome project TIGR Database. Biotechnological databases Database for species identification and classification Structural databases Database retrieval and deposition schemes
  5. 5.  What are databases? Components. Types of Databases. Applications and Limitations. Journals Publishing databases.
  6. 6.  Database management Systems ◦ Mysql ◦ Oracle ◦ Postgress ◦ Sqlserver ◦ MS Access ….
  7. 7.  A DBMS in the backend. ◦ SQL scripting ◦ PL/SQLs ◦ Other scripting interfaces(C/C++/API) A front end UI. ◦ PHP ◦ Perl/CGI ◦ VB
  8. 8.  Files are not enough Searching. Sorting. Combining data types. Organizing. Managing.
  9. 9.  Sequence data in genbank. HTML files. Excel files. Regular list. Indexes. Flat files.
  10. 10.  Biological databases ◦ MetaBase ( A database of Biological databases) ◦ http://metadatabase.org/ Bibliographic databases Chemical databases Numerous other databases.
  11. 11.  Sequence databases. ◦ Nucleotide ◦ Protein Structure Databases. Genome databases. Transcriptome databases Model organism databases. ◦ PlasmoDB, TAIR, FlyBase etc.
  12. 12.  http://asia.ensembl.org/Help/Movie?id=210
  13. 13. Genbank DDBJ EBI
  14. 14.  Gbrowse UCSC Genome Browser Vista Browser Ensembl browser Integrated Genome Browser
  15. 15.  PUBMED ◦ 22.1 million records ◦ eTBLAST CABI SCOPUS Google Scholar
  16. 16.  Organized information. Maintained and upgraded. Visualization tools.
  17. 17.  So many database to look for Not many are updated Lack of proper documentation
  18. 18.  Database Nucleic Acids Research BMC Genomics Bioinformatics Nature Cell Plant Cell
  19. 19.  Pick any database of your choice and state why you like it. (1000 characters)

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