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Bioinformatics for Vet. Part IX

Bioinformatics for Vet. Part IX. Sung Youn Lee, PhD. Student Veterinary collage, Room 320 02 450 3719, 016 293 6059 leevet@paran.com. Using the Nucleotide Sequence databases. The first sequence data bases is as sequence museum. Gene Bank

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Bioinformatics for Vet. Part IX

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  1. Bioinformatics for Vet. Part IX Sung Youn Lee, PhD. Student Veterinary collage, Room 320 02 450 3719, 016 293 6059 leevet@paran.com

  2. Using the Nucleotide Sequence databases • The first sequence data bases is as sequence museum. • Gene Bank • NCBI : U.S. National Center of Biotechnology Information • EMBL : European Molecular Biology Laboratory • DDBJ : DNA data bank of Japan

  3. Prokaryote vs Eukaryote • Single and circular DNA • A few million base (0.6-8) • 1,000bps/gene • Few useless parts (70% is protein coding part) • The genes are transcribed just right after promoter(control region) • Protein sequence are derived by ORF(open reading frame; ATG-Stop) • Promoter-RBS-ORF • Multiple linear pieces of DNA • 100,000bps/gene • Many useless parts (less than 5% is protein coding part) • The genes are transcirbed just right after promoter, but the sequence element can located far away. • The genes often exhibit more than one mRNA form.

  4. Prokaryote Gene

  5. Eukaryote Gene

  6. Prokaryotic promoter # Typical E.coli promoters – Lenhinger 1004 page

  7. Eukaryotic promoter # Eukaryotic promoter – Lenhinger 1008 page

  8. Prokaryotic gene of Gene Bank • Point ur browser to www.ncbi.nlm.nih.gov/entrez • From search pull down menu, choose nucleotide • Type X01714 and click GO

  9. Eukaryotic mRNA of Gene Bank • Point ur browser to www.ncbi.nlm.nih.gov/entrez • From search pull down menu, choose nucleotide • Type U90223 and click GO

  10. Eukaryotic genome of Gene Bank Point ur browser to www.ncbi.nlm.nih.gov/entrez From search pull down menu, choose nucleotide Type AF018430 and click GO

  11. mRNA – alternative splicing • AF018429.1:<282..561,AF018429.1:1034..1172, 560..651,AF018431.1:1..45,AF018432.1:658..732, AF018432.1:884..954,AF018432.1:1391..>1447 • Mitochondrial dUTPase mRNA • AF018429 : 282~561, 1034~1172 ; alternative splicing • AF018430 : 560~651 • AF018431 : 1~45 • AF018432 : 658~732, 884~954, 1391~1447

  12. Alternative splicing

  13. Viral genome of Gene Bank • Point ur browser to www.ncbi.nlm.nih.gov/entrez • On the black menu bar at the top of the form, click Genome. • Click the Viruses link • Type HIV2 in the search box.

  14. Bacterial genome of Gene Bank • Point ur browser to www.ncbi.nim.nih.gov/entrez • On the black menu bar at the top of the form, click Genome. • Click the Microbial link • Click which you want to get

  15. Thank you for your attention ~

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