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Bioinformatics Primer

Bioinformatics Primer. HC Lee 2000 July. What is Bioinformatics?. Biomedical/biotechnical information Reproduction and annotation of biosequences – DNA and protein Publicly accessible data banks on the web Research & computation based on data Software for such research

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Bioinformatics Primer

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  1. Bioinformatics Primer HC Lee 2000 July

  2. What is Bioinformatics? • Biomedical/biotechnical information • Reproduction and annotation of biosequences – DNA and protein • Publicly accessible data banks on the web • Research & computation based on data • Software for such research • NCBI education edu review review

  3. The Human Genome Project • WHAT? International research effort to characterize the genomes of human and selected model organisms through complete mapping and sequencing of their DNA

  4. The Human Genome Project • WHY? To develop technologies for genomic analysis, to examine the ethical, legal, and social implications of human genetics research, and to train scientists who will be able to utilize the tools and resources developed through the HGP to pursue biological studies that will improve human health

  5. The Human Genome Project • WHEN? Started in 1988 • WHERE? • First at DOE and NIH, then • National Human Genome Research Institute, National Institute of Health (USA) • Now also Europe and Japan • Many national projects • Website? HGP

  6. The Data Banks - NCBI/EMBL/DDBJ • International DNA Sequence Database Collaboration home • NCBI (GenBank) – USA (1982) homepage • EMBL – Europe (1982) homepage • DDBJ – Japan (1988) homepage

  7. Growth of Data • Began in 1982. Slow first 10 years. • First complete genome in 1995 • First billion base pair 1997 • Current – 8.2 B bp. • Double every 6 months. • GBK gbkstats • EMBL emblstats • DDBJ ddbj

  8. NCBI - National Center for Biotechnological Information Established in USA in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.

  9. GenBank – Data bank of NCBI • PubMed – publication in life sci. pubmed • Taxonomy – Tree of Life taxonomy • Structure – 3D struct of proteins structure • Entrez – databank homepage

  10. The Human Genome • 1999 December 2 • Chromosome 22 completed (47.7 Mb) • 2000 May 8 • Chromosome 21 completed (50.0 Mb) • 2000 June 26 • Working Draft of complete human genome • 97% coverage, 85% complete page

  11. A Genome • Entrez psfile • Genome query • Bacteria eubac • Haemophilus influenzae • Complete genome frame

  12. A Gene • Haemophilus influenzae • First contig qmap • First gene prot1

  13. Relatives of Gene • Homologies peptide sequences with high similarity • BLAST search webpage • Search query1 • Result AAC216

  14. Protein Data Bank • PDB homepage web • Search for protein searchlite glyceraldehyde-3-phosphate dehydrogenase • Result 1A7K • View view

  15. Human Genome Project - www.nhgri.nih.gov/HGP/ • The three main DNA banks: • GenBank - www.ncbi.nlm.nih.gov • EMBL - www.embl-heidelberg.de • DDBJ - www.ddbj.nig.ac.jp • Bioinformatics and Computational Biology sites • www.sdsc.edu/ResTools/biotools/biotools4.html#Part1 • Integrated Bioinfomatics site in TW • www2.nchc.gov.tw/~c00chh00/bioinfo.html

  16. Important protein data base- www.expasy.ch/sprot/sprot-top.html Mirror site in TW - expasy.nhri.org.tw/sprot/sprot-top.html An internet course onprotein structure www.cryst.bbk.ac.uk/pps/ The main protein databank (USA) - www.rcsb.org/pdb/ List of good links - www.rcsb.org/pdb/web-interest.html

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