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Table 4 Statistics of alignments based on sequence similarity of gene, transcript and protein comparisons

From: Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine

(A) EXAMPLE 1
  Query length Subject length Query coverage Subject coverage Identity/alig. Length Positives/alig. Length Score e-value
Solyc07g008880.2 versus VIT_09s0002g07070
 Gene vs Gene 12,772 12,589 7556/12772 7575/12589 6338/7556 6808 0
 mRNA vs mRNA 2559 2476 2289/2559 2289/2476 2152/2289 2200/2289 5385 0
 Protein vs Protein 2384 2348 2336/2384 2340/2348 2267/2343 2306/2343 4737 0
Solyc06g043160.1 versus VIT_09s0002g07070
 Gene vs Gene 159 12,589 154/159 154/12589 118/154 82 3e−15
 mRNA vs mRNA 53 2476 53/53 53/2476 43/53 47/53 111 7e−26
 Protein vs Protein 52 2348 52/52 52/2348 42/52 46/52 95 5e−24
(B) EXAMPLE 2
Solyc01g111530.2 versus VIT_03s0038g02340
 Gene vs Gene 11,273 26,647 5531/11273 5540/26647 4318/5531 3116 0
 mRNA vs mRNA 2044 1986 1681/2044 1681/1986 1287/1681 1447/1681 2927 0
 Protein vs Protein 1860 1897 1860/1860 1896/1897 1500/1914 1669/1914 2689 0
Solyc01g111530.2 versus VIT_04s0023g03830
 Gene vs Gene 11,273 10,303 3225/11273 3228/10303 2548/3225 2024 2e−98
 mRNA vs mRNA 2044 1932 1499/2044 1499/1932 1093/1499 1258/1499 2558 0
 Protein vs Protein 1860 1811 1764/1860 1799/1811 1190/1830 1407/1830 2210 0
(C) EXAMPLE 3
Solyc01g007530.2 versus VIT_10s0092g00760
 Gene vs Gene 1813 3870 1024/1813 1034/3870 910/1024 1127 0
 mRNA vs mRNA 353 318 160/353 160/318 130/160 141/160 336 4e−54
 Protein vs Protein SEQUENCE SIMILARITY NOT DETECTED
  1. The first three alignments of each example lead to the prediction of an orthology relationship by the multilevel approach proposed in this work: (A) Solyc07g008880.2 versus VIT_09s0002g07070, (B) Solyc01g111530.2 versus VIT_03s0038g02340 and (C) Solyc01g007530.2 versus VIT_10s0092g00760. The second triplets of alignments of (A) and (B) lead to the prediction of an orthology relationship by The Ensembl Plants / Gramene pipelines involving the same tomato or grapevine gene implicated in the relationship inferred by our approach (Solyc06g043160.1 versus VIT_09s0002g07070 and Solyc01g111530.2 versus VIT_04s0023g03830). Query length and query coverage are referred to the tomato gene loci, subject length and subject coverage are referred to grapevine gene loci