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Table 2 Percentage of residues left unmatched.

From: Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

   BLAT Exnrt. BLAT Exnrt.
Species Scipio (automatic assembling) with manual assembling without assembling
Bombyx mori p50T 15.03 15.41 17.03 43.61 43.64
Drosophila simulans 7.11 7.44 8.14 31.83 30.33
Bombyx mori str. Dazao 7.93 8.43 7.86 36.09 36.38
Nasonia vitripennis (contigs) 0.20 0.60 0.45 10.17 9.38
Nasonia vitripennis (scaffolds) 1.11 1.50 1.38 3.70 3.89
Drosophila sechellia 0.11 0.45 0.95 9.05 10.14
Aedes aegypti 0.73 1.01 0.21 10.43 10.22
Daphnia pulex 1.26 1.84 1.33 1.84 1.88
Anopheles gambiae 0.02 0.31 0.26 0.31 0.63
Drosophila melanogaster 0.00 0.32 0.05 0.32 0.05
Aspergillus niger 0.01 0.18 0.08 0.18 2.63
Homo sapiens 0.06 0.92 0.10 0.92 0.10
Macaca mulatta 2.29 3.09 2.31 3.09 7.82
total 1.67 2.16 1.87 8.24 8.71
  1. The percentage of residues of the query sequences that the compared tools failed to recover from the target sequence. To gain comparable results, the hits proposed by BLAT and Exonerate were assembled together manually: a collection of best-scoring non-overlapping hits was chosen for each query. The last two columns show the results if only the best-scoring hit for each query was used.