NCBI BLASTN Stage 1 in Reconfigurable Hardware

Authors

Kwame Gyang, Washington University in St. Louis

Document Type

Technical Report

Publication Date

2005-08-31

Filename

WUCSE-2005-30.pdf

Technical Report Number

WUCSE-2005-30

Abstract

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.

Comments

Permanent URL: http://dx.doi.org/10.7936/K7765CPW

Recommended Citation

Gyang, Kwame, "NCBI BLASTN Stage 1 in Reconfigurable Hardware" Report Number: WUCSE-2005-30 (2005). All Computer Science and Engineering Research.
https://openscholarship.wustl.edu/cse_research/949