OBJECTIVES
Problems
The genetic code used for the analysis can be altered by the
user
This would be important if e.g. mitochondrial or ciliate nuclear
DNA were being analysed
To overcome the limitations of ORF finder, more sophisticated
programmes detect compositional biases and increase the
reliability of gene detection
OBJECTIVES
To be able to distinguish between the concepts of ORF and gene
Use ORF Finder to find ORFs in prokaryotic nucleotide sequences
Signals - PWMs
principle is the same, signals are different
Complication of introns/exons
Eukaryotic promoter
Polyadenylation sequence
AAUAA
AUG STOP AAAAA...
~ 12bp polyA
Kozak sequence
At translational start
Introns and Exons
5Exon 3Exon
C
A
A
AGGT AGT
G ()
T
C
C
N AGG
>11
T
GT-AG rule
Exon finding
GENSCAN
FGENES
http://www.tigr.org/~salzberg/appendixa.html