NCBI BLASTN Stage 1 in Reconfigurable Hardware

Recent advances in DNA sequencing have resulted in several terabytes of DNA sequences. These sequences themselves are not informative. Biologists usually perform comparative analysis of DNA queries against these large terabyte databases for the purpose of developing hypotheses pertaining to function and relation. This is typically done using software on a general multiprocessor. However, these data sets far exceed the capabilities of the modern processor and performing sequence similarity analysis is increasingly becoming less efficient. There is an urgent need for more efficient ways of querying large DNA sequences for sequence similarities. Here, we describe an FPGA-based hardware solution that implements Stage 1 of NCBI BLASTN, a commonly used sequence analysis application

Biosequence Similarity Search on the Mercury System

Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement o# a data store and into reconfigurable hardware. An important component of application deployment on the Mercury system is the functional decomposition of the application onto both the reconfigurable hardware and the traditional processor. Both the Mercury BLASTN application design and its performance analysis are described