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Rice Data Set ???

Rice Data Set ???. Lab meeting 4-16-03. Procedures. 1.TIGR Data : >80,000 genes get mRNA 2. 1050 full length mRNA sequences from NCBI make library 3. Blast -> conseq -> percentage identity -> cut of 88% ~1038 sequences 4. combine with NCBI dna dataset: check

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Rice Data Set ???

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  1. Rice Data Set ??? Lab meeting 4-16-03

  2. Procedures 1.TIGR Data : >80,000 genes get mRNA 2. 1050 full length mRNA sequences from NCBI make library 3. Blast -> conseq -> percentage identity -> cut of 88% ~1038 sequences 4. combine with NCBI dna dataset: check gene boundary, check single exon gene 5. extend the boundary if find the match

  3. Check dataset • 1378 genes • 5.34 exons/gene • 219bp/exon • 322bp/intron • 41 incomplete • 256 single genes

  4. Problem: fgene contamination Predictions: fgene gm genscan Gene Sensitivity 78.10% 30.75% 19.36% Gene Specificity 71.75% 18.44% 15.18% Exon Sensitivity 93.74% 65.51% 35.97% Exon Specificity 90.67% 62.98% 55.20% Nucleotid Sensitivity 97.52% 84.74% 55.26% Nucleotid Specificity 95.35% 88.76% 84.51%

  5. Only NCBI Part Predictions: fgene1.list gm1.list genscan1.list Gene Sensitivity 45.95% 31.76% 21.62% Gene Specificity 42.90% 21.96% 17.58% Exon Sensitivity 80.79% 65.44% 36.52% Exon Specificity 76.58% 62.84% 53.75% Nucleotid Sensitivity 92.65% 84.04% 55.80% Nucleotid Specificity 91.87% 89.74% 85.78% 296 genes, 4.98 exons/gene, 43 single gene, 355bp/intron, 253bp/exon

  6. Not NCBI Predictions: fgene2.list gm2.list genscan2.list Gene Sensitivity 86.89% 30.47% 18.74% Gene Specificity 79.48% 17.64% 14.55% Exon Sensitivity 96.98% 65.52% 35.83% Exon Specificity 94.29% 63.02% 55.58% Nucleotid Sensitivity 98.99% 84.95% 55.10% Nucleotid Specificity 96.38% 88.47% 84.13% 1083 gene, 5.44exon/gene, 213 single genes, 210bp/exon,313bp/intron

  7. NCBI+from_Manual_clone Predictions: fgene3.list gm3.list genscan3.list Gene Sensitivity 49.72% 34.17% 24.17% Gene Specificity 46.25% 22.24% 19.59% Exon Sensitivity 82.66% 67.50% 38.68% Exon Specificity 78.38% 63.60% 56.24% NucleotideSensitivity 93.43% 85.60% 58.14% NucleotideSpecificity 92.09% 89.51% 85.62% 360 genes

  8. NCBI_Manual_all_correct Predictions: fgene4.list gm4.list genscan4.list Gene Sensitivity 54.75% 40.75% 31.75% Gene Specificity 51.29% 27.49% 26.24% Exon Sensitivity 83.88% 69.78% 42.98% Exon Specificity 79.82% 66.01% 60.56% Nucleotid Sensitivity 93.90% 86.62% 61.10% Nucleotid Specificity 92.64% 90.29% 87.07% 400genes

  9. NCBI_Manual_AllC_notfgene Predictions: fgene5.list gm5.list genscan5.list Gene Sensitivity 49.75% 35.34% 23.95% Gene Specificity 41.31% 21.23% 18.31% Exon Sensitivity 85.19% 65.39% 36.47% Exon Specificity 78.88% 62.06% 53.19% Nucleotid Sensitivity 94.49% 85.41% 57.26% Nucleotid Specificity 89.90% 86.62% 82.25% 597 genes

  10. Manual_not_fgene+allC Predictions: fgene gm genscan twinscan Gene Sensitivity 10.14% 11.05% 7.96% 15.15% Gene Specificity 9.35% 5.48% 5.52% 10.26% Exon Sensitivity 58.44% 35.94% 18.15% 49.70% Exon Specificity 59.99% 32.48% 24.69% 49.54% NucleotidSensitivity 80.09% 67.39% 46.18% 85.29% NucleotidSpecificity 82.31% 75.22% 67.79% 77.35%

  11. 99% cutoff clones • Predictions: fgene99.list • Gene Sensitivity 92.25% • Gene Specificity 86.23% • Exon Sensitivity 97.69% • Exon Specificity 94.17% • Nucleoti Sensitivity 99.49% • Nucleoti Specificity 95.50%

  12. Min’s Method on Rice cDNA set • Predictions: g++. twinscan min_001 min_02 min_min min_wei • GeneSN 40.83% 47.34% 46.75% 44.38% 46.15% 47.93% • Gene Sp 33.17% 39.90% 39.50% 37.13% 38.61% 40.40% • Exon SN 70.88% 79.36% 78.87% 76.04% 76.82% 77.53% • Exon Sp 67.72% 74.52% 75.46% 73.05% 74.97% 76.02% • NucSN 88.76% 92.11% 91.26% 90.83% 90.77% 91.72% • NucSp 89.06% 90.16% 90.17% 89.69% 90.17% 90.43%

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