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How to tell an exon from an intron?

How to tell an exon from an intron?. Overview. Using splicing enhancer WMMs Using repeat statistics Parameters and training sets Structural information. Using Splicing Enhancer (SE) WMMs. 4 WMMs derived from SELEX experiments (M. Zhang & A. Krainer labs, CSHL)

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How to tell an exon from an intron?

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  1. How to tell an exon from an intron?

  2. Overview • Using splicing enhancer WMMs • Using repeat statistics • Parameters and training sets • Structural information

  3. Using Splicing Enhancer (SE) WMMs • 4 WMMs derived from SELEX experiments (M. Zhang & A. Krainer labs, CSHL) • 6051 Refseq genes (“clean” Refseq set) • Scan introns and exons for high-scoring putative SEs. • Correlations of SE positions • Significant differences between exons and introns

  4. Pairwise distance distribution (introns)

  5. Pairwise distance distribution (exons)

  6. Using repeat statistics • ~ 90% of simple and low complexity (LC) repeats in introns are: • AT-rich • [T(A)m]n, [G(A)m]n, [C(A)m]n • Simple and LC repeats in exons are GC-rich

  7. Future Developments • Using SE WMMs with selective repeat masking • An even-periodic, 5th order Markov Model to score introns? • A new Twinscan parameter set based on “cleaner” training set

  8. Parameters and training sets • 3 “clean” Refseq sets (Randy & Sam, Jeltje, Mikhail) • Different selection criteria • Different sizes: 2 sets of ~12000 genes, 1 set of ~6000 genes • Create one training set from these 3 and re-estimate Twinscan parameters

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