Bioinformatics Algorithms: Techniques and Applications

REFERENCES 25
the flexible structure alignment FATCAT. Similar to the partial order sequence alignment,
POSA identifies structural regions that are conserved only in a subset of input
structures and allows internal rearrangements in protein structures. POSA shows its
advantages in cases in which structural flexibilities exist and provides new insights by
visualizing the mosaic nature of multiple structural alignments. POSA adopts a progressive
strategy to build a multiple structure alignment given a set of input structures
in the order provided by a guide tree. So each step involves a pairwise alignment of
two partial order alignments (or single structures), using the same formulation of AFP
chaining for structure alignment as described above, but in a high dimensional space
(see Fig. 2.6d).
2.5 SUMMARY
As one of the most commonly used algorithms in bioinformatics, dynamic
programming has been applied to many research topics. Its recent applications have
shifted from the classical topics as the comparison of linear sequences to the analysis
of nonlinear representations of biomolecules. It should be stressed that although
dynamic programming is guaranteed to report an optimal solution, this solution may
not be biologically the meaningful one. The biological solution depends not only
on the algorithm, but also on how correctly the formulation of the computational
problem reflects the reality of the biological systems.
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