文档介绍：DNA sequence analysis
Gene prediction methods
Gene indices
Mapping cDNA on genomic DNA
Genome-parison
Applications
Computational Molecular Biology
exon 2
exon 1
exon n
promotor
5‘UTR
3‘UTR
Protein coding sequence
exon n-1
DNA sequences gene structure (eucaryotes)
Computational Molecular Biology
DNA sequences repeats, repetitive elements
Long INterspersed Elements
SINE (. Alu)
Transposons
Simple repeats (. ATATA...)
Computational Molecular Biology
DNA sequences repeats, repetitive elements
High copy number
Sequence variability
Mostly located in untranslated regions
Computational Molecular Biology
Gene prediction Strategies for detecting ORFs / exons
Distribution of stop codons
Codon usage
Hexamer frequencies
Prediction of the coding frame
Splice site recognition (Eucaryotes only)
Computational Molecular Biology
Gene prediction by parison
Comparison of genomic DNA and cDNA/parison of related genomic DNA of anisms
Computational Molecular Biology
Gene prediction Codon usage (single exon)
Frame 1
Frame 2
Frame 3
coding
non-coding
Computational Molecular Biology
Gene prediction Codon usage (single exon)
Frame 1
Frame 2
Frame 3
coding
non-coding
correct start
coding sequence
Computational Molecular Biology
Gene prediction Codon usage (multiple exons)
Frame 1
Frame 2
Frame 3
coding
non-coding
Splice sites
Exons:
208. .295
1029. .1349
1500. .1688
2686. .2934
3326. .3444
3573. .3680
4135. .4309
4708. .4846
4993. .5096
7301. .7389
7860. .8013
8124. .8405
8553. .8713
9089. .9225
13841. .14244
Computational Molecular Biology