Abordagem computacional para detecção e análise de polimorfismos de nucleotídeo único em genomas bacterianos

• Autor(a) principal: Lima, Nicholas Costa Barroso
• Data de Publicação: 2011
• Tipo de documento: Dissertação
• Idioma: por
• Título da fonte: Biblioteca Digital de Teses e Dissertações do LNCC
• Texto Completo: https://tede.lncc.br/handle/tede/153
• topic: Bioinformática; Bioinformatics; CNPQ::CIENCIAS BIOLOGICAS::GENETICA

Single nucleotide polymorphism, SNP, are common and may be responsible for di_erent phenotypes. The attention around this type of polymorphism was intensi_ed when it was discovered, through the sequencing project of the human genome, that they were responsible for most of the genetic variability (90%) of complete human genomes compared. Thus, presenting a frequency of occurrence of one SNP per 1.000-2.000bp intervals. Recently, several studies have focused on the detection of this type of polymorphism in bacterial genomes for use in bacterial strain typing and phylogeny reconstruction, for example. In this work we developed a methodology for detecting and _ltering SNPs for bacterial genomes in order to analyze the prevalence of this type of polymorphism. The methodology involves the use of sequence alignment algorithms and _lters developed in PERL programming language for the detection and filtering of SNPs in order to obtain a reliable final set. The occurrence of SNPs fits the concept of Poisson probability distribution because they are events that occur in an interval, in this case, coding sequences. Within this context, we also calculated the expected frequency of SNPs for each case using a Poisson probability distribution. SNPs that exceeded the expected frequency may be subject to diferent selective pressure. The methodology was tested and evaluated for genomes in five genera of the family Enterobacteriaceae (Enterobacter, Escherichia, Salmonella, Shigella and Yersinia) and used in the case study of Klebsiella pneumoniae str. Kp13 genome, a bacteria causing nosocomial infection. The methodology has been able to detect and filter SNPs in diferent species of the family Enterobacteriaceae in accordance with data already published. For the four Klebsiella pneumoniae strains analyzed the occurrence of such polymorphism between the strains compared was observed. Thus, coding sequences with a number of SNPs higher than the expected frequency, obtained by the Poisson Probability Distribution, have been investigated to assess its possible association with the bacteria lifestyle.