Indexing and Retrieval for Genomic Databases
IEEE Transactions on Knowledge and Data Engineering
FLASH: A Fast Look-Up Algorithm for String Homology
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
A New Hardware Architecture for Genomic and Proteomic Sequence Alignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
A New Hardware Architecture for Genomic and Proteomic Sequence Alignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Biosequence Similarity Search on the Mercury System
Journal of VLSI Signal Processing Systems
Acceleration of ungapped extension in Mercury BLAST
Microprocessors & Microsystems
Probabilistic Methods for Bioinformatics: with an Introduction to Bayesian Networks
Probabilistic Methods for Bioinformatics: with an Introduction to Bayesian Networks
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In this paper we present our genomic and proteomic sequence alignment algorithm, DASH, which results in order of magnitude speed improvement when compared to NCBIBLAST 2.2.6 [1], with superior sensitivity. Dynamic programming (DP) is the predominant contributor to search time for algorithms such as BLAST and FastA/P [2]. Improving the efficiency of DP provides an opportunity to increase sensitivity, or significantly reduce search times and help offset the effects of the continuing exponential growth in database sizes. Specifically, for nucleotide searching we have demonstrated an order of magnitude speed improvement with significantly improved sensitivity, or alternatively moderate speed up with further sensitivity gains, depending on the parameters selected. Smith-Waterman [3] complete DP is used as the sensitivity benchmark. Similar speed and sensitivity results are presented for protein searching. Since our algorithm is highly parallel, we have developed dedicated hardware which we will present in a companion paper [4], and a distributed version of our software (DDASH), which we expect to provide linear speedup on a cluster.