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 NCBI education edu review reviewedureview

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

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

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? HGPHGP

The Data Banks - NCBI/EMBL/DDBJ International DNA Sequence Database Collaboration homehome –NCBI (GenBank) – USA (1982) homepagehomepage –EMBL – Europe (1982) homepagehomepage –DDBJ – Japan (1988) homepagehomepage

Growth of Data Began in Slow first 10 years. First complete genome in 1995 First billion base pair 1997 Current – 8.2 B bp. Double every 6 months. GBK gbkstatsgbkstats EMBL emblstatsemblstats DDBJ ddbjddbj

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.

GenBank – Data bank of NCBI PubMed – publication in life sci. pubmedpubmed Taxonomy – Tree of Life taxonomytaxonomy Structure – 3D struct of proteins structurestructure Entrez – databank homepagehomepage

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 pagepage

A Genome Entrez psfilepsfile –Genome queryquery –Bacteria eubaceubac Haemophilus influenzae –Complete genome frameframe

A Gene Haemophilus influenzae –First contig qmapqmap »First gene prot1prot1

Relatives of Gene Homologies peptide sequences with high similarity BLAST search webpagewebpage –Search query1query1 –Result AAC216AAC216

Protein Data Bank PDB homepage webweb Search for protein searchlitesearchlite glyceraldehyde-3-phosphate dehydrogenase –Result 1A7K1A7K View viewview

Human Genome Project - The three main DNA banks: GenBank - EMBL - DDBJ - Bioinformatics and Computational Biology sites Integrated Bioinfomatics site in TW www2.nchc.gov.tw/~c00chh00/bioinfo.html

Important protein data base- top.html Mirror site in TW - expasy.nhri.org.tw/sprot/sprot-top.html An internet course onprotein structure The main protein databank (USA) - List of good links -