منابع مشابه
pp-Blast: a "pseudo-parallel" Blast.
We have developed a software called pp-Blast that uses the publicly available Blast package and PVM (parallel virtual machine) to partition a multi-sequence query across a set of nodes with replicated or shared databases. Benchmark tests show that pp-Blast running in a cluster of 14 PCs outperformed conventional Blast running in large servers. In addition, using pp-Blast and the cluster we were...
متن کاملParallel BLAST on split databases
SUMMARY BLAST programs often run on large SMP machines where multiple threads can work simultaneously and there is enough memory to cache the databases between program runs. A group of programs is described which allows comparable performance to be achieved with a Beowulf configuration in which no node has enough memory to cache a database but the cluster as an aggregate does. To achieve this r...
متن کاملDynamic BLAST – a Grid Enabled BLAST
Basic Local Alignment Search Tool (BLAST) is a heavily used bioinformatics application that has gotten significant attention from the high performance computing community. The authors have taken BLAST execution a step further and enabled it to execute on grid resources. Adapting BLAST to execute on the grid brings up concerns regarding grid resource heterogeneity, which inevitably cause difficu...
متن کاملG-BLAST: A Grid Service for BLAST
This paper described the design and implementation of G-BLAST – a Grid Service for one of the most widely used bioinformatics application Basic Local Alignment Search Tool (BLAST). G-BLAST uses the factory design pattern to provide application developers a common interface to incorporate multiple implementations of BLAST. The process of application selection, resource selection, scheduling, and...
متن کاملParallel BLAST Analysis and Performance Evaluation
BLAST is an efficient heuristic algorithm used for comparing biological sequences, such as amino-acids or nucleotides and identifying similarities between them. However, extensive genetic mapping projects feed sequence databases continuously, forcing them to grow steadily, turning execution time into a potential constraint to sequential implementations of the algorithm and driving the search fo...
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ژورنال
عنوان ژورنال: Brazilian Journal of Medical and Biological Research
سال: 2003
ISSN: 0100-879X
DOI: 10.1590/s0100-879x2003000400007