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Graphical alignment of sequences through parallel programming: an approach from the post-genomic era
Alineamiento gráfico de secuencias a través de programación paralela: un enfoque desde la era postgenómica
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Graphical alignment of sequences through parallel programming: an approach from the post-genomic era. (2020). Revista Ingeniería Biomédica, 13(26). https://doi.org/10.24050/19099762.n26.2019.1404
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A graphical alignment or “dot plot” is a method of visual representation of genomic data analysis, commonly used to compare the similarity of two biological sequences. The DOTTER program, developed in 1995, is the most widely used tool for this type of task. The biggest problem with this software is the high runtime for large scale genomic data. GEPARD (2007), performs faster alignments for larger sequences than DOTTER, but reducing the execution time of the alignment of a chromosome against itself, from 382 years with DOTTER to 61 minutes with GEPARD, although with a low level of detail because it uses an approximation method. This article proposes a strategy that works on multiple processors to perform genomic-level alignments in a shorter run time than GEPARD, achieving accelerations up to 27.9 times using 64 processors from the nominal value. The strategy allows the identification of chromosomal rearrangements, repetitive elements, comparison between genomes of different species and the graphic measurement of the assembly quality of genomic sequences quickly.
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