Databases Part II

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Course material for aCSIR Ph.D Programs

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Databases Part II

  1. 1. Sucheta Tripathy,
  2. 2.  Mid term: ◦ 20 marks  14 marks  8 for evaluations  6 for test  6 marks Meets the character specification (+1) Answers the Question (+1) Originality (+1) Clarity/perspective (+1) Copy from someone/internet (-1)
  3. 3.  Encyclopedia of life (www.eol.org ) Education + EOL (http://education.eol.org ) http://indiabiodiversity.org
  4. 4.  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.
  5. 5. 17 countries out of XXX contains 70% biodiversity: “Megadiverse”
  6. 6. India Bio diversity
  7. 7. The Bar Code of Life (BOLD Systems)International Barcode of Life ProjectsData Portal; Barcode Cluster; Data Collection V3 is released: V2 will be maintained till 2012 Dec.
  8. 8.  Animal Identification ◦ COI (cytochrome C oxidase subunit 1) Fungi Identification ◦ (ITS – internal transcribed spacer) Plant Identification ◦ Rbcl (ribulose bisphosphate carboxylase) ◦ Mat k (maturase k)
  9. 9. http://www.youtube.com/watch?v=ZImiXgU6bCk&feature=related
  10. 10. •Genbank •Entrez •CoreNucleotide •DbEST •dbGSS •NCBI-eutilities
  11. 11. Data Retrieval and depositionschemes •NCBI-eutilitieshttp://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=cancer&reldate=60&datetype=edat&retmax=100&usehistory=yhttp://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=19923,12120Ref:http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
  12. 12. Data Retrieval and depositionschemes 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

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