MAVID: Constrained Ancestral Alignment of Multiple Sequences

Table 1.

Comparison of MLAGAN and MAVID Multiple Alignments on the 21 Organism CFTR Alignment

MAVID Zebrafish
96
96
68
68
64
72
96
96
96
96
96
96
96
96
96
96
96
96
96
96
MLAGAN Zebrafish 96 32 12 12 8 8 12 12 12 12 12 12 12 12 12 12 12 12 12 12
MAVID Dunnart - 88 88 41 41 41 71 71 71 71 88 88 88 88 88 88 88 88 88 88
MLAGAN Dunnart - 88 88 59 0 0 0 0 0 0 88 88 88 88 88 88 88 88 88 88
MAVID Platypus - - 51 51 52 51 49 51 49 51 51 51 52 52 52 52 52 52 51 51
MLAGAN Platypus - - 40 40 25 34 34 34 36 37 51 51 51 51 51 51 51 51 51 36
MAVID Hedgehog - - - 46 46 46 56 57 57 57 67 67 64 66 66 66 66 67 60 60
MLAGAN Hedgehog - - - 74 74 74 74 74 73 76 66 64 63 63 63 63 63 63 63 69
MAVID Chicken - - - - 79 86 90 79 83 83 81 71 71 76 76 71 71 71 69 69
MLAGAN Chicken - - - - 38 69 67 67 69 74 74 74 74 74 74 74 74 74 74 67
MAVID Rat - - - - - 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100
MLAGAN Rat - - - - - 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100
MAVID Fugu - - - - - - 84 84 85 85 85 88 88 88 88 88 88 88 85 85
MLAGAN Fugu - - - - - - 22 22 22 22 42 48 48 48 48 48 48 48 48 41
MAVID Cow - - - - - - - 100 100 100 100 100 100 100 100 100 100 100 100 100
MLAGAN Cow - - - - - - - 100 100 100 100 100 100 100 100 100 100 100 100 100
MAVID Rabbit - - - - - - - - 96 95 95 95 95 95 95 94 94 94 94 94
MLAGAN Rabbit - - - - - - - - 90 90 90 90 90 90 90 90 90 90 90 90
MAVID Dog - - - - - - - - - 100 100 100 100 100 100 100 100 100 100 100
MLAGAN Dog - - - - - - - - - 100 100 100 100 100 100 100 100 100 100 100
MAVID Opossum - - - - - - - - - - 90 92 92 92 92 92 90 92 92 92
MLAGAN Opossum - - - - - - - - - - 74 74 72 72 72 72 72 72 72 78
MAVID Tetraodon - - - - - - - - - - - 88 88 88 88 88 88 88 85 85
MLAGAN Tetraodon - - - - - - - - - - - 48 48 48 48 48 48 48 48 40
MAVID Lemur - - - - - - - - - - - - 100 100 100 100 100 100 100 100
MLAGAN Lemur - - - - - - - - - - - - 100 100 100 100 100 100 100 100
MAVID Horse - - - - - - - - - - - - - 100 100 100 100 100 100 100
MLAGAN Horse - - - - - - - - - - - - - 100 100 100 100 100 100 100
MAVID Pig - - - - - - - - - - - - - - 100 100 100 100 100 100
MLAGAN Pig - - - - - - - - - - - - - - 100 100 100 100 100 100
MAVID Cat - - - - - - - - - - - - - - - 100 100 100 100 100
MLAGAN Cat - - - - - - - - - - - - - - - 100 100 100 100 100
MAVID Mouse - - - - - - - - - - - - - - - - 100 100 100 100
MLAGAN Mouse - - - - - - - - - - - - - - - - 100 100 100 100
MAVID Baboon - - - - - - - - - - - - - - - - - 100 100 100
MLAGAN Baboon - - - - - - - - - - - - - - - - - 100 100 100
MAVID Macaque - - - - - - - - - - - - - - - - - - 92 92
MLAGAN Macaque - - - - - - - - - - - - - - - - - - 96 96
MAVID Chimp - - - - - - - - - - - - - - - - - - - 100
MLAGAN Chimp
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
100

  • Each row in the table shows the % coverage of the alignable exons in an organism as calculated by extracting the pairwise alignment with human from the multiple alignment. The different columns in the table correspond to the number of sequences in the multiple alignment. Thus, the first column corresponds to the pairwise alignment of human-zebrafish and the last column to the multiple alignment of all 21 sequences. Organisms were added according to the k-MST, so that the alignment problems are as difficult as possible (mutually most distant organisms).

This Article

  1. Genome Res. 14: 693-699

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