Publication

A Rate-based Prefiltering Approach to BLAST Acceleration

Abstract

DNA sequence comparison and database search have evolved in the last years as a field of strong competition between several reconfigurable hardware computing groups. In this paper we present a BLAST preprocessor that efficiently marks the parts of the database that may produce matches. Our prefiltering approach offers significant reduction in the size of the database that needs to be fully processed by BLAST, with a corresponding reduction in the run-time of the algorithm. We have implemented our architecture, evaluated its effectiveness for a variety of databases and queries, and compared its accuracy against the original NCBI Blast implementation. We have found that prefiltering offers at least a factor of 5 and up to 3 orders of magnitude reduction in the database space that needs to be fully searched. Due to its prefiltering nature, our approach can be combined with all major reconfigurable acceleration architectures that have been presented up to date.

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Related concepts (28)
Database
In computing, a database is an organized collection of data (also known as a data store) stored and accessed electronically through the use of a database management system. Small databases can be stored on a , while large databases are hosted on computer clusters or cloud storage. The design of databases spans formal techniques and practical considerations, including data modeling, efficient data representation and storage, query languages, security and privacy of sensitive data, and distributed computing issues, including supporting concurrent access and fault tolerance.
Competition
Competition is a rivalry where two or more parties strive for a common goal which cannot be shared: where one's gain is the other's loss (an example of which is a zero-sum game). Competition can arise between entities such as organisms, individuals, economic and social groups, etc. The rivalry can be over attainment of any exclusive goal, including recognition. Competition occurs in nature, between living organisms which co-exist in the same environment. Animals compete over water supplies, food, mates, and other biological resources.
Competition law
Competition law is the field of law that promotes or seeks to maintain market competition by regulating anti-competitive conduct by companies. Competition law is implemented through public and private enforcement. It is also known as antitrust law (or just antitrust), anti-monopoly law, and trade practices law; the act of pushing for antitrust measures or attacking monopolistic companies (known as trusts) is commonly known as trust busting. The history of competition law reaches back to the Roman Empire.
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