Overestimation for Multiple Sequence Alignment

9 years 8 months ago
Overestimation for Multiple Sequence Alignment
Abstract— Multiple sequence alignment is an important problem in computational biology. A-star is an algorithm that can be used to find exact alignments. We present a simple modification of the A-star algorithm that improves much multiple sequence alignment, both in time and memory, at the cost of a small accuracy loss. It consists in overestimating the admissible heuristic. A typical speedup for random sequences of length two hundred fifty is 47 associated to a memory gain of 13 with an error rate of 0.09%. Concerning real sequences, the speedup can be greater than 13,000 and the memory gain greater than 150, the error rate being in the range from 0.08% to 0.71% for the sequences we have tested. Overestimation can align sequences that are not possible to align with the exact algorithm.
Tristan Cazenave
Added 02 Jun 2010
Updated 02 Jun 2010
Type Conference
Year 2007
Authors Tristan Cazenave
Comments (0)