biological databases

Introduction to Databases

Sucheta Tripathy7th October 2012

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.

Recap

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

Assignment

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

Topics To be taught

What are databases? Components. Types of Databases. Applications and Limitations. Journals Publishing databases.

Topics to be covered

Database management Systems◦ Mysql◦ Oracle◦ Postgress◦ Sqlserver◦ MS Access ….

What are databases?

A DBMS in the backend.◦ SQL scripting◦ PL/SQLs◦ Other scripting interfaces(C/C++/API)

A front end UI.◦ PHP◦ Perl/CGI◦ VB

Components

Files are not enough Searching. Sorting. Combining data types. Organizing. Managing.

When you Need a Database?

Sequence data in genbank. HTML files. Excel files. Regular list. Indexes. Flat files.

Commonly Used Databases that are not…

Biological databases◦ MetaBase ( A database of Biological databases)◦ http://metadatabase.org/

Bibliographic databases Chemical databases Numerous other databases.

Types of Databases

Sequence databases.◦ Nucleotide◦ Protein

Structure Databases. Genome databases. Transcriptome databases Model organism databases.

◦ PlasmoDB, TAIR, FlyBase etc.

Biological Databaseshttp://en.wikipedia.org/wiki/List_of_biological_databases

Nucleotide Databases

Nucleotide Databases (TIGR)

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

Ensembl Genome Projectwww.ensembl.org

Nucleotide Databases

Nucleotide Databases

Genbank

DDBJ

EBI

Gbrowse UCSC Genome Browser Vista Browser Ensembl browser Integrated Genome Browser

Genome Browsers

PUBMED◦ 22.1 million records◦ eTBLAST

CABI SCOPUS Google Scholar

Bibliographic databases

Organized information. Maintained and upgraded. Visualization tools.

Advantages of Databases

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

Dis-advantages of Databases

Database Nucleic Acids Research BMC Genomics Bioinformatics Nature Cell Plant Cell

Database journals

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

Assignment