Antonio Espinosa

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Traditional parallel programming forces the programmer, apart from designing the application, to analyse the performance of this recently built application. This dljjjcult task of testing the behaviour of the program can be avoided with the use of an automatic performance analysis tool. Users are released from having to understand the enormous amount of(More)
Approximate string matching is a very important problem in computational biology; it requires the fast computation of string distance as one of its essential components. Myers' bit-parallel algorithm improves the classical dynamic programming approach to Levenshtein distance computation, and offers competitive performance on CPUs. The main challenge when(More)
Fast pattern matching is a requirement for many problems, specially for bioinformatics sequence analysis like short read mapping applications. This work presents a variation of the FM-index method, denoted n-step FM-index, that is applied in exact match genome search. We propose an alternative two-dimensional FM-index structure that allows backward-search(More)
1 Actual behaviour of parallel programs is of capital importance for the development of an application. Programs will be considered matured applications when their performance is under acceptable limits. Traditional parallel programming forces the programmer to understand the enormous amount of performance information obtained from the execution of a(More)
We describe the use of non-dedicated clusters by a known group of local applications sharing the computational resources with additional bioinformatics MapReduce applications. We have studied how to effectively use the resources shared by both application types during their execution. In order to keep local application execution times unaffected we consider(More)