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Table 2 Test scenario 1: Reconstruction of the Loxodonta africana dynein heavy chain genes in the whole genome sequence based on human protein sequences

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

Tool Predicted genes Missing exons1 Wrong exons2 Exon sens. % Exon sens. (ov.)3 % Exon spec. % Nucl. sens. % Nucl. spec. % Execution time per prot. seq.
Scipio 1.54 16 11 6 93.4 99.1 93.3 98.7 99.8 70 m 46s
Exonerate5 2145 6 5669 94.8 99.5 16.5 99.7 18.5 123 m 23s
Exonerate6 16 287 62 73.4 76.1 90.2 76.1 94.3 121 m 27s
Augustus7 1374928 0 3909434 47.9 100.0 0.0 100.0 0.3 > 10 days
BLAT8 - 9 264228 19.6 99.3 0.1 97.4 2.6 7 m 24s
Scipio 1.04 16 14 46 86.1 98.8 83.2 97.9 99.4 8 m 24s
  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 Parameters: --model protein2genome
  6. 6 Parameters: --model protein2genome --bestn 1
  7. 7 Parameters: --species = human --genemodel = exactlyone (for more parameters see Additional file 5)
  8. 8 Parameters as in 4: -tileSize = 7 -minIdentity = 54 -minScore = 15 -oneOff = 1