Enabling HMMER for the Grid with COMP Superscalar

Abstract The continuously increasing size of biological sequence databases has motivated the development of analysis suites that, by means of parallelization, are capable of performing faster searches on such databases. However, many of these tools are not suitable for execution on mid-to-large scale parallel infrastructures such as computational Grids. This paper shows how COMP Superscalar can be used to effectively parallelize on the Grid a sequence analysis program. In particular, we present a sequential version of the HMMER hmmpfam tool that, when run with COMP Superscalar, is decomposed into tasks and run on a set of distributed resources, not burdening the programmer with parallelization efforts. Although performance is not a main objective of this work, we also present some test results where COMP Superscalar, using a new pre-scheduling technique, clearly outperforms a well-known parallelization of the hmmpfam algorithm.