1. ”Gene Finding in Eukaryotic Genomes”
DTU course #27011
Nikolaj Blom
Center for Biological Sequence Analysis BioCentrum-DTU
Technical University of Denmark

2. Today’s plan
Lecture on gene finding
Gene features, Repeatmasker, etc.
Get notebooks (building 208; secretary)+Pause
Work on project
Nikolaj present from
Lars present from

3. Practical Stuff Webpage, Literature, Textbooks Report writing format
Contribution from each student specified
E.g. Lars & Dorte mainly wrote the Introduction and Methods: Lise & Jens wrote the Results and Discussion sections
Repeatmasker

4. Gene Features Codon frequency/bias Transcriptional Exon/introns
Organism dependent
Hexamer statistics
Transcriptional
Promoters/enhancers
Exon/introns
Length distributions
ORFs
Splicing
Donor/acceptor sites
Branchpoints
Translational
Start codon context

5. Codon Bias tRNA availability Expression level
Gene Finders are often organism specific
Coding regions often modelled by 5th order Markov chain (hexamers/di-codons)

6. Human genes:
Short exons
Long introns

7. Human genes:
Introns lengths have broad distribution
Min. Length ca. 60 bp

8. Intron Prevalence

10. Gene Prediction – Performance of Genscan

11. NIX – Visualizing Gene Predictions
NO method is always best!

12. Performance of Genscan – Exon Length
Low performance at short exon lengths

13. Future Challenges
Bootstrapping: prediction improves as more genes become known
’Extreme’ genes (long/short) still difficult
Initial and terminal exons are predicted with lower confidence
Combine with Sequence Similarity Matches
Non-coding RNAs
Most gene prediction programs only predict protein-coding genes
tRNA and rRNA genes are not predicted
Predict alternatice splicing, enhancers and silencers
Predict matrix- and scaffold-attachment regions, insulators and boundary elements

14. Gene Prediction Take home messages Prediction methods are not perfect!
Genes may be predicted by computer programs
Masking of repetitive sequences may be required for large genomic sequences
’Unusual’ genes are difficult (high GC%, short or terminal exons)
HMM-based gene prediction programs are suitable for “Gene Grammar”
Prediction methods are not perfect!

15. Repeatmasker
Repetitive sequences in human/eukaryotic genomes are a problem
Run gene predictions on large genomic regions before and after masking of repetitive sequence:
Up to 45% of human genomic sequence derived from transposable/repetitive elements

16. Repeatmasker http://www.repeatmasker.org/
Screens DNA sequences for interspersed repeats and low complexity DNA sequences
Matches against database of known repeat elements
Repeats in genomic sequence may cause wrong gene predictions

18. Select ”html” format

19. >chr19_not_repeatmasked hg16_dna range=chr19: 'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=none
AGGTGTGTTGGCACACGCCTGTAATCCCAGCTACTGAGGAGGCTGAGGCATGAGAATCGCTTGAACCTGAGAGGCGGAGGTTGTAGTGAGTCGAGATTGCACCACTGCACTCCAGCCTGGGTGACAAAGTGAGACCCTGTCTCAAAAAAAAAAAAAAAAAAAAAGTGAATGTTCCACAGCATCACAGATGAATTTTGCAAATATGTTGCATGAAAGAAGAATAAACACTCTGTGATTCCATTTATTTAAACTATAAAAACAAGGAGAGCTAATTTATGCTGTTAGAGGAGTGGTTGCTTTGGGGTATGGGGAGGGGGTGGCAAGGATTAGTGACTGTCGTGGGCCCAAGTGGGGTTTCAGGGGTGCTGGCATTATTCCATCTCTTGGTCTGGGTGCTGGTCCTGTAGGGTATGTTCAGTCTGAAAATCCATCCCACCAGACATTTACGAATCATGCCCTTTCCTGGGTGTATATTATACATCAATAACAATTTTTTTTTTTTTTTGAGATGGAGTCTTGCTTTGTTGCCCAGGCTGGAGTGCAGTGGTGCAGTCTCCACCTCCCAGATTTAAGTGATTCTCATACCTCAGCCTCCCTAGTAGCTGGGATTACAGGCGTGTGCCACCACACCTGGCTCATTTTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCATGGTGAAACTTTGAAGGCCAATGGTGAAACATGAGGCCAAACTCCTGGCCTCAAGTGGTCCACCCACCT
>chr19_repeatmasked hg16_dna range=chr19: 'pad=0 3'pad=0 revComp=FALSE strand=? repeatMasking=N
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnGTGAATGTTCnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

20. Repetitive Elements LINE = Long interspersed elements
______
45%
LINE = Long interspersed elements
SINE = Short interspersed elements

24. The End