Figure 8.

Example: alternative splicing. Simulated example of protein sequences along the given phylogeny containing independent insertions at the same site in region A, a long insertion in region B, and alternative splicings in regions C and D. All tested methods have problems with the alignment of the flanking regions (B) of the long insertion and Prank+F fails to align the alternative splicings correctly, as they are not consistent with the phylogeny. Regions C and D are aligned almost correctly by Prank except for the Aspartic acid (red circle) of region C aligned to region D. The independent insertions in region A are detected correctly by ProGraphMSA and Prank+F due to their phylogenetically-aware algorithms.

Szalkowski BMC Bioinformatics 2012 13:129   doi:10.1186/1471-2105-13-129
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