TY - GEN

T1 - Parallel progressive Multiple Sequence Alignment

AU - Pitzer, Erik

PY - 2005

Y1 - 2005

N2 - Multiple Sequence Alignment is an essential tool in the analysis and comparison of biological sequences. Unfortunately, the complexity of this problem is exponential. Currently feasible methods are, therefore, only approximations. The progressive multiple sequence alignment algorithms are the most widespread among these approximations. Still, the computation speed of typical problems is often not satisfactory. Hence, the well known progressive alignment scheme of ClustalW has been subject to parallelization to further accelerate the computation. In the course of this action a unique scheme to parallelize sequence alignment in particular and dynamic programming in general was discovered, which yields an average of n/2 parallel calculations for problem size n. The scalability of O(n) tasks for problem size n can be even maintained for slower networks.

AB - Multiple Sequence Alignment is an essential tool in the analysis and comparison of biological sequences. Unfortunately, the complexity of this problem is exponential. Currently feasible methods are, therefore, only approximations. The progressive multiple sequence alignment algorithms are the most widespread among these approximations. Still, the computation speed of typical problems is often not satisfactory. Hence, the well known progressive alignment scheme of ClustalW has been subject to parallelization to further accelerate the computation. In the course of this action a unique scheme to parallelize sequence alignment in particular and dynamic programming in general was discovered, which yields an average of n/2 parallel calculations for problem size n. The scalability of O(n) tasks for problem size n can be even maintained for slower networks.

UR - http://www.scopus.com/inward/record.url?scp=33645989980&partnerID=8YFLogxK

U2 - 10.1007/11556985_61

DO - 10.1007/11556985_61

M3 - Conference contribution

AN - SCOPUS:33645989980

SN - 3540290028

SN - 9783540290025

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 473

EP - 482

BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

T2 - 10th International Conference on Computer Aided Systems Theory - EUROCAST 2005

Y2 - 7 February 2005 through 11 February 2005

ER -