Gene and alternative splicing annotation with AIR

Table 5.

Performance of three methods for mapping cross-species evidence with varying evolutionary distances, exemplified at the CFTR locus in human and 12 other species

Exon (full)
V = 0
V = 10
Exon (partial)
Splice junctions
Bp
Species
Toola
 Sn/Sp
Sn/Sp
Sn/Sp
Sn/Sp
Sn/Sp
Baboon AIR 0.985 0.971 0.993 0.978 1.000 0.985 1.000 0.984 1.000 0.996
BLASTZ 0.015 0.015 0.739 0.728 1.000 0.985 0.073 0.071 0.997 0.945
sim4 0.955 0.941 0.985 0.971 1.000 0.985 0.992 0.976 0.978 0.995
Cat AIR 0.963 0.970 0.963 0.970 1.000 1.000 0.976 0.984 0.999 0.985
BLASTZ 0.030 0.030 0.726 0.736 0.985 0.985 0.080 0.080 0.994 0.945
sim4 0.881 0.804 0.896 0.818 1.000 0.985 0.984 0.891 0.954 0.997
Chicken AIR 0.359 0.583 0.359 0.583 0.615 1.000 0.455 0.714 0.297 0.992
BLASTZ 0 0 0.590 0.622 0.949 1.000 0.030 0.032 0.744 0.662
sim4 0.359 0.368 0.436 0.447 0.769 0.857 0.545 0.562 0.420 0.964
Chimp AIR 0.991 0.974 0.991 0.974 1.000 0.982 1.000 0.981 1.000 0.981
BLASTZ 0.027 0.026 0.750 0.718 1.000 0.957 0.078 0.075 0.997 0.942
sim4 0.973 0.948 0.991 0.965 1.000 0.974 1.000 0.971 1.000 0.980
Cow AIR 0.924 0.924 0.955 0.955 1.000 1.000 0.959 0.959 0.996 0.994
BLASTZ 0.015 0.015 0.758 0.752 0.992 0.992 0.082 0.081 0.996 0.952
sim4 0.848 0.762 0.894 0.803 1.000 0.978 0.967 0.861 0.904 0.991
Dog AIR 0.922 0.905 0.942 0.924 1.000 0.981 0.958 0.938 0.996 0.892
BLASTZ 0.019 0.019 0.738 0.717 0.990 0.971 0.084 0.082 0.997 0.891
sim4 0.835 0.723 0.883 0.765 1.000 0.920 0.947 0.811 0.895 0.940
Fugu AIR 0 0 0 0 0 0 0 0 0 0
BLASTZ 0.030 0.050 0.396 0.662 0.612 1.000 0.081 0.143 0.663 0.939
sim4 0.073 0.129 0.173 0.306 0.473 0.929 0.230 0.418 0.203 0.977
Mouse AIR 0.838 0.838 0.875 0.875 0.993 0.993 0.944 0.944 0.943 0.957
BLASTZ 0.015 0.015 0.625 0.620 0.978 0.993 0.040 0.039 0.931 0.907
sim4 0.713 0.602 0.765 0.646 0.985 0.950 0.889 0.742 0.757 0.967
Pig AIR 0.942 0.942 0.951 0.951 1.000 1.000 0.968 0.968 0.997 0.998
BLASTZ 0.029 0.029 0.718 0.705 0.990 0.981 0.053 0.052 0.995 0.953
sim4 0.903 0.795 0.932 0.821 1.000 0.972 0.979 0.853 0.913 0.995
Rat AIR 0.824 0.830 0.853 0.859 0.985 0.993 0.913 0.920 0.927 0.952
BLASTZ 0.029 0.029 0.610 0.610 0.971 0.992 0.048 0.048 0.920 0.913
sim4 0.691 0.573 0.779 0.646 0.993 0.978 0.897 0.734 0.735 0.970
Tetraodon AIR 0 0 0 0 0 0 0 0 0 0
BLASTZ 0.060 0.099 0.448 0.741 0.604 0.976 0.097 0.167 0.664 0.957
sim4 0.105 0.186 0.177 0.314 0.403 0.833 0.219 0.403 0.208 0.957
Zfish AIR 0 0 0 0 0 0 0 0 0 0
BLASTZ 0 0 0.395 0.586 0.814 1.000 0.054 0.087 0.785 0.868
sim4
0.053
0.080
0.263
0.400
0.658
1.000
0.176
0.286
0.437
0.976

  • The evaluation was performed at exon, splice junction, and base-pair level. A full-exon match requires that both exon boundaries agree within V bp, whereas a partial-exon match only requires that the exons overlap. Sensitivity is measured as Sn = TP/(TP + FN), specificity as Sp = TP/(TP + FP) (Burset and Guigo 1996).

  • ↵a (AIR) Synteny-based feature tracking; (BLASTZ) direct alignment of the cDNA sequence and the genomic region; (sim4) splice-sensitive cDNA-to-genome alignment

This Article

  1. Genome Res. 15: 54-66

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