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Table 3 Test scenario 2: Reconstruction of the Loxodonta africana dynein heavy chain gene structures in the respective gene regions based on human protein sequences

From: Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio

Tool Pred. genes Missing exons1 Wrong exons2 Exon sens. % Exon sens. (ov.)3 % Exon spec. % Nucl. sens. % Nucl. spec. %
Scipio 1.54 16 13 6 93.1 98.9 93.1 98.6 99.8
Scipio 1.55 16 4 7 94.7 99.7 93.7 99.2 99.8
Prosplign6 16 1 41 95.7 99.9 92.6 99.9 98.7
Exonerate7 32 7 6 94.8 99.4 94.6 99.6 99.5
Exonerate8 16 255 4 75.7 78.8 95.6 79.2 99.7
Prot_map9 16 4 27 91.7 99.7 86.2 99.3 99.7
Fgenesh+10 16 10 10 94.9 99.2 94.8 99.0 99.7
Wise211 39 3 16 93.3 99.8 91.2 99.7 98.9
Augustus12 16 132 111 81.9 89.0 83.2 89.9 88.7
Fgenesh10 161 111 342 80.2 90.8 67.3 91.8 62.3
Genscan13 194 138 520 76.3 88.5 57.9 90.4 55.3
BLAT14 - 16 19 19.9 98.7 19.4 97.0 98.9
Scipio 1.04 16 16 10 86.2 98.7 85.9 97.8 99.8
  1. 1 Number of annotated exons, which are not overlapped by any predicted exon
  2. 2 Number of predicted exons, which are not overlapped by any annotated exon
  3. 3 Number annotated exons, which are overlapped by at least one predicted exon divided by the number of annotated exons
  4. 4 Mammalia cross species default options (for detailed parameters see Additional file 5)
  5. 5 Mammalia cross species default options; -tileSize = 6 (for detailed parameters see Additional file 5)
  6. 6 Parameters: -full -two_stages
  7. 7 Parameters: --model protein2genome
  8. 8 Parameters: --model protein2genome --bestn 1
  9. 9 Similarity: Weak; Search for one best alignment only (for more parameters see Additional file 5)
  10. 10 Organism: Human
  11. 11 Parameters: -both
  12. 12 Parameters: --species = human --genemodel = exactlyone (for more parameters see Additional file 5)
  13. 13 Organism: Vertebrate; Suboptimal exon cutoff: 1.00
  14. 14 Parameters as in 4: -tileSize = 7 -minIdentity = 54 -minScore = 15 -oneOff = 1