Biological databases
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Transcript of Biological databases
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Introduction to Databases
Sucheta Tripathy7th October 2012
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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
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Write a paragraph (less than 1000 characters) on “why you think more genomes need to be sequenced OR not sequenced”.
[email protected]/[email protected]
Assignment
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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
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What are databases? Components. Types of Databases. Applications and Limitations. Journals Publishing databases.
Topics to be covered
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Database management Systems◦ Mysql◦ Oracle◦ Postgress◦ Sqlserver◦ MS Access ….
What are databases?
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A DBMS in the backend.◦ SQL scripting◦ PL/SQLs◦ Other scripting interfaces(C/C++/API)
A front end UI.◦ PHP◦ Perl/CGI◦ VB
Components
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Files are not enough Searching. Sorting. Combining data types. Organizing. Managing.
When you Need a Database?
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Sequence data in genbank. HTML files. Excel files. Regular list. Indexes. Flat files.
Commonly Used Databases that are not…
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Biological databases◦ MetaBase ( A database of Biological databases)◦ http://metadatabase.org/
Bibliographic databases Chemical databases Numerous other databases.
Types of Databases
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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
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Nucleotide Databases
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Nucleotide Databases (TIGR)
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http://asia.ensembl.org/Help/Movie?id=210
Ensembl Genome Projectwww.ensembl.org
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Nucleotide Databases
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Nucleotide Databases
Genbank
DDBJ
EBI
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Gbrowse UCSC Genome Browser Vista Browser Ensembl browser Integrated Genome Browser
Genome Browsers
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PUBMED◦ 22.1 million records◦ eTBLAST
CABI SCOPUS Google Scholar
Bibliographic databases
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Organized information. Maintained and upgraded. Visualization tools.
Advantages of Databases
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So many database to look for Not many are updated Lack of proper documentation
Dis-advantages of Databases
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Database Nucleic Acids Research BMC Genomics Bioinformatics Nature Cell Plant Cell
Database journals
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Pick any database of your choice and state why you like it. (1000 characters)
Assignment