The Genome Access Course

1
The Genome Access Course
Gene Prediction
2
We took this
3
(No Transcript)
4
and did this
5
(No Transcript)
6
Now we want this
7
Eukaryotic Genomes
8
and this
9
(No Transcript)
10
and this
11
(No Transcript)
12
and this
13

14
from this
15
Raw Genome Data
16
(No Transcript)
17
Definition of GeneWhat are genes?

• Prokaryotic - ORFs
• Eukaryotic Introns/Exons

18
Lets do some!

• Address www.dnalc.org/bioinformatics/
• tgac_uwe_gene_prediction.htm
• Exercises 1 and 2
• Link

19
Eukaryotic Genes
20

• Definition
• vs.
• Concept

21
A Dynamic Concept

• Introns/exons
• Postransriptional modifications
• Alternative splicing
• Differential expression
• Genes-in-genes
• Genes-ad-genes
• Postranslational modifications
• Multi-subunit proteins

22
From raw sequence to a gene
23
Gene Prediction

• Distinguish coding/non-coding
• sequences
• Homology-based (similarity)
• Ab initio (content signals)
• Combinations

24
Gene Prediction Flow

• Identify promising regions (nucleotides)
• Narrow down genes (nucleotides, codons)
• Narrow down structure (promotor, polyA-site)
• Determine structure (exons, CDSs)
• Determine transcripts (alternative splicing)

25
Motif Finding Splice Sites

• Ex ATCAG GTTTG In TTCAG TGCAC Ex
• Ex TGTTG GTAAG In CTCAG ACTGA Ex
• Ex CAGAG GTGAG In TCCAG GAATT Ex
• Ex ATAAG GTAAT In TGCAG CTCGG Ex

26
Motif Finding Splice Sites

• Ex ATCAG GTTTG In TTCAG TGCAC Ex
• Ex TGTTG GTAAG In CTCAG ACTGA Ex
• Ex CAGAG GTGAG In TCCAG GAATT Ex
• Ex ATAAG GTAAT In TGCAG CTCGG Ex

27
Lets watch some movies

• www.dnalc.org/bioinformatics/Movies/tata1.swf
• www.dnalc.org/bioinformatics/Movies/tata2.swf

28
In reality
29
Motif Extracter

• Address
• http//www-btls.jst.go.jp/
• Link

30
Lets do some more!

• Address www.dnalc.org/bioinformatics/t
• gac_uwe_gene_prediction.htm
• Exercises 3 and 4
• Link