DNA Sequencing

The sequencing of the Human Reference Genome, with Human Genome Project announced ten years ago, provided a roadmap that is the foundation for modern biomedical research. Reference Genome represents digital database founded by scientists which contains representative examples of species genomes. The need for sequencing has never been greater than it is today. Sequencing has found its applications within diverse research sectors including comparative genomics and evolution, forensics, epidemiology, and applied medicine for diagnostics and therapeutics. Arguably, the strongest rationale for ongoing sequencing is the question for identification and interpretation of human sequence variation as it relates to health and disease. The paper gives review of current DNA sequencing algorithms and techniques as well as next-generation of DNA sequencing. Since the DNA sequencing field is changing rapidly the information in this paper represent a snapshot of this particular moment

Implementación de un programa en lenguaje Perl para el ensamblaje de secuencias nucleotídicas

En este trabajo, hemos creado un programa que permite el ensamblaje de novo de secuencias nucleotídicas. El programa ha sido escrito en lenguaje de programación Perl y utiliza una estrategia basada en la representación de la secuencia mediante un grafo bidirigido de De Bruijn. A partir de secuencias nucleotídicas de pequeño tamaño (las lecturas), el programa produce un archivo en formato FastA con las secuencias de los cóntigos producto del ensamblaje y otro en formato dot con una representación gráfica de la relación existente entre dichos cóntigos. Hemos utilizado el programa para evaluar los efectos de varios parámetros (como la longitud de los k-meros, la cobertura o la tasa de error en las lecturas) sobre la calidad de los ensamblajes resultantes. Además, hemos comprobado que los grafos de De Bruijn son una herramienta interesante para detectar variantes en el procesamiento de los intrones. Por último, consideramos que nuestro programa representa una herramienta docente muy poderosa para que los estudiantes exploren la relación entre la Teoría de Grafos y la GenómicaIn this work, we have written a computer program for the de novo assembly of nucleotide sequences. The program has been written using the Perl programming language, and uses a strategy based on bidirected de Bruijn graphs. Starting from short nucleotide sequences (the reads), the program produces a FastA file containing the contig sequences and a dot file that allows one to visualize the relationship among the different contigs. We have used our program in order to evaluate the effects of several parameters (such as the k-mer length, the sequencing coverage or the sequencing error rates) on the quality of the resulting assemblies. In addition, we have found that De Bruijn graphs are an interesting tool that might facilitate the identification of novel splice variants. Finally, we think that our program is a powerful teaching tool that will help the students to investigate the relationships between graph theory and genomic