RESUMO
Resumen La alineación de ADN es un proceso clave para la reconstrucción de genomas, a partir de los millones de lecturas cortas producidas por las máquinas de secuenciación paralela masiva. Tal proceso suele realizarse mediante algoritmos con elevada complejidad espacial y temporal, requiriendo varias horas para entregar los resultados, así como decenas de GB de RAM. Esto ha motivado la búsqueda de nuevos algoritmos y/o estrategias que permitan disminuir los tiempos de ejecución, mientras se utilizan recursos mínimos de memoria. En este artículo se presenta ABPSE, un nuevo alineador de ADN que combina el algoritmo de Ferragina y Manzini (o índices de FM) y el algoritmo de Myers, mediante la estrategia siembra y extiende. En la siembra, los índices de FM permiten calcular de manera rápida regiones con alta probabilidad de alineación; mientras que en la extensión, el algoritmo de Myers refina la alineación utilizando operaciones basadas en vectores de bits, calculando simultáneamente varias celdas de la matriz de programación dinámica. Los resultados muestran un 96.1% de lecturas alineadas correctamente, un factor de aceleración de 2.45x en relación a BWA-SW y un uso de memoria de apenas 7.6 GB, cuando se alinea el genoma humano completo.
Abstract DNA alignment is a key process in the assembly of genomes from the millions of short reads that are produced by massive parallel sequencing machines. Such a process is usually done by means of high spatial and temporal complexity algorithms, which takes hours to deliver the results as well as tens of GB of RAM. This has prompted the search for new algorithms and/or strategies that allow shorter runtimes, while using minimal memory footprint. In this article, we present ABPSE, a new DNA aligner that combines the Ferragina and Manzini algorithm (or FM indexes) and the Myers algorithm, by means of the seed and extend strategy. In the seeding, the FM indices allow a rapid calculation of the regions with high probability of alignment. In the extension, the Myers algorithm refines the alignment using operations based on bit vectors. It simultaneously calculates several cells of the dynamic programming matrix. The results show 96.1% of correctly aligned reads, an acceleration factor of 2.45x in relation to BWA-SW and a memory footprint of only 7.6 GB when aligning the entire human genome.
RESUMO
The human gastroenteritis caused by Campylobacter jejuni in some industrialized countries is higher than gastroenteritis produced by Salmonella and Shigella. This has induced the development of techniques to demonstrate the presence of the microorganism in different foods using some culture media combinations. There is not a method to isolate C. jejuni from roasted chicken and fried pork meat, which are popular foods in México. The sensitivity of two culture media combinations was compared: Rama broth (RB)-Rama agar (RA) and Preston broth (PB)-Skirrow agar (SA) to isolate C. jejuni from these foods. The RB-RA combination demonstrated to be the best one to isolate C. jejuni.