Parallel characteristics of sequence alignment algorithms
Proceedings of the 1989 ACM/IEEE conference on Supercomputing
Principles of distributed database systems (2nd ed.)
Principles of distributed database systems (2nd ed.)
Parallel Computation in Biological Sequence Analysis
IEEE Transactions on Parallel and Distributed Systems
A Database Index to Large Biological Sequences
Proceedings of the 27th International Conference on Very Large Data Bases
Information Management for Genome Level Bioinformatics
Proceedings of the 27th International Conference on Very Large Data Bases
Efficient Data Access for Parallel BLAST
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Papers - Volume 01
IEEE Transactions on Parallel and Distributed Systems
A case study of parallel I/O for biological sequence search on Linux clusters
International Journal of High Performance Computing and Networking
BLAST Distributed Execution on Partitioned Databases with Primary Fragments
High Performance Computing for Computational Science - VECPAR 2008
Parallel genome sequence searching on SupercomputerBlueGene/P
ECS'10/ECCTD'10/ECCOM'10/ECCS'10 Proceedings of the European conference of systems, and European conference of circuits technology and devices, and European conference of communications, and European conference on Computer science
Parallel performance evaluation of sequence nucleotide alignment on the supercomputer BlueGene/P
ECC'11 Proceedings of the 5th European conference on European computing conference
Parallelism in bioinformatics workflows
VECPAR'04 Proceedings of the 6th international conference on High Performance Computing for Computational Science
Performance analysis of applying replica selection technology for data grid environments
PaCT'05 Proceedings of the 8th international conference on Parallel Computing Technologies
| Hi-index | 0.00 |
In this work we investigate the parallel evaluation of BLAST, the most popular tool for comparing biological sequences. Our goal is to study database distribution issues that, besides workload balancing, could improve the performance of a set of BLAST processes running in a workstation cluster. We consider different partitioning strategies within actual BLAST executions against a few relevant molecular databases. We have implemented multiple databases and input sequence configurations and show that there are many important parameters, such as the fragment generation method and sequence similarities, that must be taken into account in order to make full use of such parallel environment.