Biological databases
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Biological databases

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Course work on biological databases

Course work on biological databases

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  • 1. Sucheta Tripathy7th October 2012
  • 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.  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.  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.  What are databases? Components. Types of Databases. Applications and Limitations. Journals Publishing databases.
  • 6.  Database management Systems ◦ Mysql ◦ Oracle ◦ Postgress ◦ Sqlserver ◦ MS Access ….
  • 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.  Files are not enough Searching. Sorting. Combining data types. Organizing. Managing.
  • 9.  Sequence data in genbank. HTML files. Excel files. Regular list. Indexes. Flat files.
  • 10.  Biological databases ◦ MetaBase ( A database of Biological databases) ◦ http://metadatabase.org/ Bibliographic databases Chemical databases Numerous other databases.
  • 11.  Sequence databases. ◦ Nucleotide ◦ Protein Structure Databases. Genome databases. Transcriptome databases Model organism databases. ◦ PlasmoDB, TAIR, FlyBase etc.
  • 12.  http://asia.ensembl.org/Help/Movie?id=210
  • 13. Genbank DDBJ EBI
  • 14.  Gbrowse UCSC Genome Browser Vista Browser Ensembl browser Integrated Genome Browser
  • 15.  PUBMED ◦ 22.1 million records ◦ eTBLAST CABI SCOPUS Google Scholar
  • 16.  Organized information. Maintained and upgraded. Visualization tools.
  • 17.  So many database to look for Not many are updated Lack of proper documentation
  • 18.  Database Nucleic Acids Research BMC Genomics Bioinformatics Nature Cell Plant Cell
  • 19.  Pick any database of your choice and state why you like it. (1000 characters)