Parallel processing of biological sequence comparison algorithms
International Journal of Parallel Programming
A space-efficient parallel sequence comparison algorithm for a message-passing multiprocessor
International Journal of Parallel Programming
A linear space algorithm for computing maximal common subsequences
Communications of the ACM
Parallel Biological Sequence Comparison Using Prefix Computations
IPPS '99/SPDP '99 Proceedings of the 13th International Symposium on Parallel Processing and the 10th Symposium on Parallel and Distributed Processing
Space and Time Optimal Parallel Sequence Alignments
IEEE Transactions on Parallel and Distributed Systems
Parallel syntenic alignment on GPUs
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
| Hi-index | 0.00 |
Given two genomic DNA sequences, the syntenic alignment problem is to compute an ordered list of subsequences for each sequence such that the corresponding subsequence pairs exhibit a high degree of similarity. Syntenic alignments are useful in comparing genomic DNA from related species andin identifying conservedgen es. In this paper, we present a parallel algorithm for computing syntenic alignments that runs in O(mn/p) time and O(m + n/p) memory per processor, where m and n are the respective lengths of the two genomic sequences. Our algorithm is time optimal with respect to the corresponding sequential algorithm and can use O(n/log n) processors, where n is the length of the larger sequence. Using an implementation of this parallel algorithm, we report the alignment of human chromosome 12p13 and its syntenic region in mouse chromosome 6 (both over 220, 000 base pairs in length) in under 24 minutes on a 64-processor IBM xSeries cluster.