Databases IISucheta Tripathy,

Mid term:◦ 20 marks

14 marks 8 for evaluations 6 for test

6 marks

Evaluations

Meets the character specification (+1)Answers the Question (+1)Originality (+1)Clarity/perspective (+1)Copy from someone/internet (-1)

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

http://indiabiodiversity.org

Plant and Animal Databases

The Encyclopedia of Life is a collaborative effort among scientist and the general public to bring information together about all 1.9 million named and known species, in a common format, freely available on the internet.

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