PPCAS: Implementation of a Probabilistic Pairwise Model for Consistency-Based Multiple Alignment in Apache Spark
MetadataShow full item record
Large-scale data processing techniques, currently known as Big-Data, are used to manage the huge amount of data that are generated by sequencers. Although these techniques have significant advantages, few biological applications have adopted them. In the Bioinformatic scientific area, Multiple Sequence Alignment (MSA) tools are widely applied for evolution and phylogenetic analysis, homology and domain structure prediction. Highly-rated MSA tools, such as MAFFT, ProbCons and T-Coffee (TC), use the probabilistic consistency as a prior step to the progressive alignment stage in order to improve the final accuracy. In this paper, a novel approach named PPCAS (Probabilistic Pairwise model for Consistency-based multiple alignment in Apache Spark) is presented. PPCAS is based on the MapReduce processing paradigm in order to enable large datasets to be processed with the aim of improving the performance and scalability of the original algorithm.
Is part ofLecture Notes in Computer Science, 2017, vol. 10393, p. 601–610
European research projects
Showing items related by title, author, creator and subject.
Lladós Segura, Jordi; Cores Prado, Fernando; Guirado Fernández, Fernando (Springer, 2019)With the advent of new high-throughput next-generation sequencing technologies, the volume of genetic data processed has increased significantly. It is becoming essential for these applications to achieve large-scale alignments ...
High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools Orobitg Cortada, Miquel; Guirado Fernández, Fernando; Cores Prado, Fernando; Lladós Segura, Jordi; Notredame, Cedric (Elsevier, 2014-10-08)Multiple Sequence Alignment (MSA) is essential for a wide range of applications in Bioinformatics. Traditionally, the alignment accuracy was the main metric used to evaluate the goodness of MSA tools. However, with the ...
Lladós Segura, Jordi; Cores Prado, Fernando; Guirado Fernández, Fernando; Lérida Monsó, Josep Lluís (Elsevier, 2021)Background and Objective: The emergence of Next-Generation sequencing has created a push for faster and more accurate multiple sequence alignment tools. The growing number of sequences and their longer sizes, which require ...