An I/O device driver for bioinformatics tools: the case for BLAST

Renato Campos Mauro, Sérgio Lifschitz
Published September 30, 2005
Genet. Mol. Res. 4 (3): 563-570 (2005)

About the Authors
Renato Campos Mauro, Sérgio Lifschitz

Corresponding author
S. Lifschitz


There are many bioinformatics tools that deal with input/ output (I/O) issues by using filing systems from the most common operating systems, such as Linux or MS Windows. However, as data volumes increase, there is a need for more efficient disk access, ad hoc memory management and specific page-replacement policies. We propose a device driver that can be used by multiple applications. It keeps the application code unchanged, providing a non-intrusive and flexible strategy for I/O calls that may be adopted in a straightforward manner. With our approach, database developers can define their own I/O management strategies. We used our device driver to manage Basic Local Alignment Search Tool (BLAST) I/O calls. Based on preliminary experimental results with National Center for Biotechnology Information (NCBI) BLAST, this approach can provide database management systems-like data management features, which may be used for BLAST and many other computational biology applications.

Key words: BLAST, Driver, Databases.

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