Sharif Digital Repository

In the mid twentieth century by discovering the existence of genetic strands and understanding their role in diseases and phenotypes of species, research initiated to decipher their content. Sequencing of the first human genome at early twenty-first century paved the way to study and even cure complex human deseases having genetic origin. Next Generation Sequencing (NGS) Technologies have significantly reduced the expenses and the timing complexity of DNA Sequencing and this has an improving trend. In this thesis, we evaluate Base Calling methods, a critical step in analyzing next generation sequencing information and deals with massive sequencing data. Base Calling tries to optimally detect... 

Genome sequencing is one of the fundamental problems in today’s Biology. It has applications in significant problems such as finding association between an individual’s genome sequence and his phenotypes, discovering new genes, and finding evolutionary relations between organisms. Following the rapid advances in sequencing technologies and generation of a huge amount of short reads, efficient computational tools are needed for processing sequencing data. Shortness of reads is a factor that makes the task of reconstructing repetitive genomic regions complicated. In fact, the main challenge in both sequencing and resequencing problems is reconstruction of repeat regions. Common resequencing... 

DNA sequence is the lifetime private information of each individual: it can reveal personal traits, health status, and medical risk of that individual, it can be abused by entities such as insurance companies, it can be used for identity theft, etc. Unfortunately, due to cost, regulations, or some restrictions, we may not be able to complete DNA sequencing in-house and have to outsource it to some unreliable companies in some foreign countries.This would compromise the DNA privacy from the beginning. This would raise the question that how we can guarantee the DNA privacy in the process of sequencing.Here we propose a solution for private DNA sequencing by exploiting the fact that the process...