Course work on biological databases

1. Sucheta Tripathy
7th 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.

14.  http://asia.ensembl.org/Help/Movie?id=210

16. Genbank DDBJ
EBI

17.  Gbrowse
 UCSC Genome Browser
 Vista Browser
 Ensembl browser
 Integrated Genome Browser

18.  PUBMED
◦ 22.1 million records
◦ eTBLAST
 CABI
 SCOPUS
 Google Scholar

19.  Organized information.
 Maintained and upgraded.
 Visualization tools.

20.  So many database to look for
 Not many are updated
 Lack of proper documentation

21.  Database
 Nucleic Acids Research
 BMC Genomics
 Bioinformatics
 Nature
 Cell
 Plant Cell

22.  Pick any database of your choice and state
why you like it. (1000 characters)