# A sparse dynamic programming algorithm for alignment with non-overlapping inversions

Alair Pereira do Lago; Ilya Muchnik; Casimir Kulikowski

RAIRO - Theoretical Informatics and Applications (2010)

- Volume: 39, Issue: 1, page 175-189
- ISSN: 0988-3754

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topAlair Pereira do Lago, Muchnik, Ilya, and Kulikowski, Casimir. "A sparse dynamic programming algorithm for alignment with non-overlapping inversions." RAIRO - Theoretical Informatics and Applications 39.1 (2010): 175-189. <http://eudml.org/doc/92754>.

@article{AlairPereiradoLago2010,

abstract = {
Alignment of sequences is widely used for biological sequence
comparisons, and only biological events like mutations, insertions
and deletions are considered. Other biological events like
inversions are not automatically detected by the usual alignment
algorithms, thus some alternative approaches have been tried in order
to include inversions or other kinds of rearrangements.
Despite many important results in the last decade, the complexity of the
problem of alignment with inversions is still unknown. In 1992, Schöniger
and Waterman proposed the simplification hypothesis that the inversions do
not overlap. They also presented an O(n6) exact solution for
the alignment with non-overlapping inversions problem and introduced a
heuristic for it that brings the average case complexity down. (In this work, n is the maximal
length of both sequences that are aligned.)
The present paper gives two exact algorithms for the simplified
problem. We give a quite simple dynamic program with O(n4)-time
and O(n2)-space complexity for alignments with non-overlapping
inversions and exhibit a sparse and exact implementation version of
this procedure that uses much less resources for some applications
with real data.
},

author = {Alair Pereira do Lago, Muchnik, Ilya, Kulikowski, Casimir},

journal = {RAIRO - Theoretical Informatics and Applications},

language = {eng},

month = {3},

number = {1},

pages = {175-189},

publisher = {EDP Sciences},

title = {A sparse dynamic programming algorithm for alignment with non-overlapping inversions},

url = {http://eudml.org/doc/92754},

volume = {39},

year = {2010},

}

TY - JOUR

AU - Alair Pereira do Lago

AU - Muchnik, Ilya

AU - Kulikowski, Casimir

TI - A sparse dynamic programming algorithm for alignment with non-overlapping inversions

JO - RAIRO - Theoretical Informatics and Applications

DA - 2010/3//

PB - EDP Sciences

VL - 39

IS - 1

SP - 175

EP - 189

AB -
Alignment of sequences is widely used for biological sequence
comparisons, and only biological events like mutations, insertions
and deletions are considered. Other biological events like
inversions are not automatically detected by the usual alignment
algorithms, thus some alternative approaches have been tried in order
to include inversions or other kinds of rearrangements.
Despite many important results in the last decade, the complexity of the
problem of alignment with inversions is still unknown. In 1992, Schöniger
and Waterman proposed the simplification hypothesis that the inversions do
not overlap. They also presented an O(n6) exact solution for
the alignment with non-overlapping inversions problem and introduced a
heuristic for it that brings the average case complexity down. (In this work, n is the maximal
length of both sequences that are aligned.)
The present paper gives two exact algorithms for the simplified
problem. We give a quite simple dynamic program with O(n4)-time
and O(n2)-space complexity for alignments with non-overlapping
inversions and exhibit a sparse and exact implementation version of
this procedure that uses much less resources for some applications
with real data.

LA - eng

UR - http://eudml.org/doc/92754

ER -

## References

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