Bioinformatics for Vet. Part IXBioinformatics for Vet. Part IX

Sung Youn Lee, PhD. StudentSung Youn Lee, PhD. StudentVeterinary collage, Room 320Veterinary collage, Room 32002 450 3719, 016 293 605902 450 3719, 016 293 6059

leevet@paran.comleevet@paran.com

Using the Nucleotide Using the Nucleotide Sequence databasesSequence databases

The first sequence data bases The first sequence data bases is as sequence museum.is as sequence museum.

Gene BankGene Bank NCBI : U.S. National Center of NCBI : U.S. National Center of

Biotechnology InformationBiotechnology Information EMBL : European Molecular EMBL : European Molecular

Biology LaboratoryBiology Laboratory DDBJ : DNA data bank of JapanDDBJ : DNA data bank of Japan

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 th

an 5% is protein coding part)• The genes are transcirbed ju

st right after promoter, but the sequence element can located far away.

• The genes often exhibit more than one mRNA form.

Prokaryote Gene

Eukaryote Gene

Prokaryotic promoter

# Typical E.coli promoters – Lenhinger 1004 page

Eukaryotic promoter

# Eukaryotic promoter – Lenhinger 1008 page

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

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

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

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

Alternative splicing

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.

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

Thank you for your attention ~Thank you for your attention ~