The document discusses various types of biological databases including sequence databases, structure databases, genome databases, and model organism databases. It provides examples of nucleotide databases like Genbank, DDBJ, EMBL-EBI, and TIGR. Genome browsers like UCSC Genome Browser, Ensembl browser, and Integrated Genome Browser are also mentioned. Other topics covered include the Encyclopedia of Life, India Biodiversity, Barcode of Life, data retrieval schemes, bibliographic databases, and database journals.

1. Sucheta Tripathy,

2.  Biological databases
◦ MetaBase ( A database of Biological databases)
◦ http://metadatabase.org/
 Bibliographic databases
 Chemical databases
 Numerous other databases.
Types of Databases

3.  Sequence databases.
◦ Nucleotide
◦ Protein
 Structure Databases.
 Genome databases.
 Transcriptome databases
 Model organism databases.
◦ PlasmoDB, TAIR, FlyBase etc.
Biological Databases
http://en.wikipedia.org/wiki/List_of_biological_databases

4.  NA and protein databases.
 Animal and plant databases
 Ensembl Genome project
 TIGR Database.
 Biotechnological databases
 Database for species identification and
classification
 Database retrieval and deposition schemes
 Literature search databases
Topics To be taught

5. Nucleotide Databases

6. Nucleotide Databases (TIGR)
Founded Celera Genomics
to fund Shot gun
sequencing.
Created a synthetic
organism called
as Mycoplasma
laboratorium

7. Nucleotide Databases

8. Nucleotide Databases (INSDC)
Genbank DDBJ
EBI

9. Data type DDBJ EMBL-EBI NCBI
Next
generation
reads
Sequence
Read Archive
European
Nucleotide
Archive
(ENA)
Sequence
Read Archive
Capillary
reads
Trace Archive Trace Archive
Annotated
sequences
DDBJ GenBank
Samples BioSample BioSample
Studies BioProject BioProject
Nucleotide Databases (INSDC)
http://www.insdc.org/documents/feature-table

10.  http://asia.ensembl.org/Help/Movie?id=210
 http://ensemblgenomes.org/
Ensembl Genome Project
www.ensembl.org

11.  Gbrowse
 UCSC Genome Browser
 Vista Browser
 Ensembl browser
 Integrated Genome Browser (IGV)
Genome Browsers

12.  Encyclopedia of life (www.eol.org )
 Education + EOL (http://education.eol.org )
 http://indiabiodiversity.org

13.  Trusted comprehensive information on every
species on earth.
 Has about 2 million pages and each page
catalogues a species.
 Community driven.

17. 17 countries out of XXX contains 70% biodiversity: “Megadiverse”

18. India Bio diversity

20. The Bar Code of Life (BOLD Systems)
International Barcode of Life Projects
V3 is released: V2 will be maintained till 2012 Dec.
Data Portal; Barcode Cluster; Data Collection

21.  Animal Identification
◦ COI (cytochrome C oxidase subunit 1)
 Fungi Identification
◦ (ITS – internal transcribed spacer)
 Plant Identification
◦ Rbcl (ribulose bisphosphate carboxylase)
◦ Mat k (maturase k)

23. http://www.youtube.com/watch?v=ZImiXgU6bCk&feature=related

24. •Genbank
•Entrez
•CoreNucleotide
•DbEST
•dbGSS
•NCBI-eutilities

25. Data Retrieval and deposition
schemes
•NCBI-eutilities
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed
&term=cancer&reldate=60&datetype=edat&retmax=100&usehistory=
y
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleoti
de&term=biomol+trna[prop]
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein
&term=70000:90000[molecular+weight]
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=struc
ture&id=19923,12120
Ref:
http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch

26. Data Retrieval and deposition
schemes
BankIt : Single or a simple group of sequences: web based
Sequin : Simple to complex submission ; < 10,000 sequences
Tbl2Asn : Template File; Sequence file; Feature Table

27.  PUBMED
◦ 22.1 million records
◦ eTBLAST
 CABI
 SCOPUS
 Google Scholar
Bibliographic databases

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