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8-20-2003 Lab meeting

8-20-2003 Lab meeting. Ping Hu. Arabidopsis thaliana predictions (5.25E). Separation of the final At predictions. Total Prediction (30634). Exactly as annotation(15063). Not as annotation(15588). Overlap with confirmed annotation(3246). Not overlap with confirmed ann (12342).

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8-20-2003 Lab meeting

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  1. 8-20-2003 Lab meeting Ping Hu

  2. Arabidopsis thaliana predictions (5.25E)

  3. Separation of the final At predictions Total Prediction (30634) Exactly as annotation(15063) Not as annotation(15588) Overlap with confirmed annotation(3246) Not overlap with confirmed ann (12342) Not overlap with any ann( 4394) Overlap with other ann (7948) Same start/Same stop 2358 Diff start/Same stop 2770 Same start/Diff stop 1879 Diff start/Diff stop 941 Same Exon Struct 945 Diff Exon Struct 1825 Same Exon Struct 165 Diff Exon Struct 1714

  4. Comparision with the corrent annotation

  5. The GC/AG and GT/AG splice sites • GC/AG introns represent 0.7% of total human pre-mRNA introns; ~0.6% in C. elegans (Nuc Acid Research 30(15) 3360-3368). • 252/33350=0.75% in Arabidopsis • 27/2034 = 1.3% in crypto • Twinscan can not predict the GC donor site

  6. Simple Model: one more level of DT Donor sites G1T2 G1C2 G1T2G5 G1T2H5 G1T2G5G-1 G1T2G5H-1 G1T2G5G-1A-2 G1T2G5G-1B-2 G1T2G5G-1A-2T6 G1T2G5G-1A-2S6

  7. Performance on Arabidopsis

  8. Performance on Crypto

  9. Performance on Crypto

  10. Future Direction • Experiment test of the At prediction • Improve the rice prediction • GC gradient • Start stop model • Different Codon usage matrix • Annotation

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