An I/O device driver for bioinformatics tools: the case for BLAST.
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.
Mauro
Renato Campos
RC
Departamento de Informática PUC-RIO, Pontifícia Universidade Católica do Rio de Janeiro, Rua Marquês de São Vicente, 225 Gávea, 22453-900 Rio de Janeiro, RJ, Brazil.
Lifschitz
Sérgio
S
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D016208:Databases, Factual; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*