Sharif Digital Repository

Human is diploid specie that inherits a set of chromosomes from their mother and a set from their father. The process of separating the nucleotide content of a set of extracted maternal and paternal chromosomes for an individual or a population is called phasing the genome of the individual or the population. The placement of any two variants relative to each other in diploid species is possible in two forms: cis (placement of both variants on one chromosome), and trans (placement of variants on different chromosomes). Each of these conditions leads to different phenotypes. Thus, understanding how variants are placed relative to each other is a crucial problem in human biology which is... 

One of the branches of genetic studies is population genetics. Each population has its own characteristics due to its evolutionary history, cultural characteristics and geography, which distinguish it from other populations. Scientific and technological advances in recent decades have led to the production of new generation sequencing machines and the creation of large genetic data. These data contain important genetic information and answers to many questions about the origin of humans, the history of populations and their evolutionary process. More and better understanding of the human genome and the distance between populations can help to better understand biological mechanisms and deal... 

Recently, portable genome sequencing devices have been introduced to the market, which have also made it possible to provide these services in remote locations or outside the laboratory. The amount of raw data from the readings of a sequencer for the entire genome of a human or plant can be in the hundreds of gigabytes, making it difficult and expensive to maintain and transfer to the center for such sequencing. Fortunately, these readings have a lot of redundancy, and many new algorithms have been proposed to compress them based on the intrinsic properties of this data. Sequencing devices were mainly used in the laboratory environment, which naturally had virtually unlimited access to urban... 

Nowadays, one of the challenges in the field of bioinformatics is the excess processed data volume such that this data volume resulted from a complete genome sequence of a species can be up to hundreds gigabytes. Every time that we talk about increasing data volume, data storage, transforming, and the process will become of interest. Moreover, considering the presence of portable sequencer devices in the market and the limitations of process outside of the lab environments, this problem becomes of more critical importance. Fortunately, due to the nature of the genome data and their redundancy, specific algorithms to compress them have been introduced to the market. In this thesis, we chose... 

Humans, as a diploid species, have two nucleotide sequences of homologous chromosomes in their genomes, where one set is inherited from the mother, and the other comes from the father. The Single Individual Haplotype assembly problem (SIH) refers to the reconstruction of these two distinct nucleotide sequences of a chromosome from the sequencing reads, and it is currently considered one of the most important issues in the field of computational genomics, which plays an essential role in solving various genetic and medical problems.Nowadays direct experimental methods are not welcomed due to their high cost, and labor intensity, and are limited to certain regions of the genome, therefore,... 

Bacteria are the first organisms, and ath the same time, the most diverse forms of life that appeared on the earth and without their functions living on the earth would not be possible. Therefore, recognition of bacteria is greatly important and can lead to the recognition of new genes, production of new antibiotics and anti-cancer compounds, etc. The problem of identifying the bacterial genome from DNA sequences obtained directly from environmental samples is known as Metagenomics. One of the main stages of Metagenomics is the binning of genetic components and because bio-marker based binning methods are only able to bin 1% of bacterial species, bio-marker free methods have been considered... 

The classification of biological sequences is an open issue for a variety of data sets, such as viral and metagenomics sequences. Therefore, many studies utilize neural network tools, as the well-known methods in this field, and focus on designing customized network structures. However, a few works focus on more effective factors, such as input encoding method or implementation technology, to address accuracy and efficiency issues in this area. Therefore, in this work, we propose an image-based encoding method, called as WalkIm, whose adoption, even in a simple neural network, provides competitive accuracy and superior efficiency, compared to the existing classification methods (e.g. VGDC,... 

One of the most available genomics data in Iran is non-invasive parental testing (NIPT) data obtained from the blood of pregnant mothers after the tenth week of pregnancy using the new generation sequencing technology. Sequencer output is a combination of maternal and fetal read data, most of which (about 90%) is from maternal DNA. These data have very low coverage of the genome, but their advantage is that they read the entire human genome. Low coverage data has led to the loss of large parts of the genome, but having a large number of samples helps to compensate for this problem. The purpose of this project is to use this data with the help of imputation methods to build a reference for...