Databases ii

Databases IISucheta Tripathy,

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

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

Nucleotide Databases

Nucleotide Databases (TIGR)

Founded Celera Genomics to fund Shot gun sequencing.Created a synthetic organism called as  Mycoplasma laboratorium

Nucleotide Databases

Nucleotide Databases (INSDC)

Genbank DDBJ

EBI

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

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

Ensembl Genome Projectwww.ensembl.org

Gbrowse UCSC Genome Browser Vista Browser Ensembl browser Integrated Genome Browser (IGV)

Genome Browsers

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

http://indiabiodiversity.org

Plant and Animal Databases

Trusted comprehensive information on every species on earth.

Has about 2 million pages and each page catalogues a species.

Community driven.

Encyclopedia Of Life

India Bio diversity

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

India Bio diversity

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

Animal Identification◦ COI (cytochrome C oxidase subunit 1)

Fungi Identification◦ (ITS – internal transcribed spacer)

Plant Identification◦ Rbcl (ribulose bisphosphate carboxylase)◦ Mat k (maturase k)

Barcode Of Life

Barcode of life

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

Data Retrieval and deposition schemes

•Genbank•Entrez

•CoreNucleotide•DbEST•dbGSS

•NCBI-eutilities

Data Retrieval and deposition schemes

•NCBI-eutilitieshttp://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=nucleotide&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=structure&id=19923,12120

Ref: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch

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

PUBMED◦ 22.1 million records◦ eTBLAST

CABI SCOPUS Google Scholar

Bibliographic databases

Database Nucleic Acids Research BMC Genomics Bioinformatics Nature Cell Plant Cell

Database journals