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metagenomics
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WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs
, Article PLoS ONE ; Volume 17, Issue 4 April , 2022 ; 19326203 (ISSN) ; Mohammadi, A ; Koohi, S ; Sharif University of Technology
Public Library of Science
2022
Abstract
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,...
A Novel Method to Improve Binning of Metagenomic Sequence Fragments by Using Gene Ontology Graphs
, M.Sc. Thesis Sharif University of Technology ; Beigy, Hamid (Supervisor) ; Marashi, Amir (Supervisor)
Abstract
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...
DNA Classification Using Optical Processing based on Alignment-free Methods
, M.Sc. Thesis Sharif University of Technology ; Koohi, Somayyeh (Supervisor)
Abstract
In this research, an optical processing method for DNA classification is presented in order to overcome the problems in the previous methods. With improving in the operational capacity of the sequencing process, which has increased the number of genomes, comparing sequences with a complete database of genomes is a serious challenge to computational methods. Most current classification programs suffer from either slow classification speeds, large memory requirements, or both. To achieve high speed and accuracy at the same time, we suggest using optical processing methods. The performance of electronic processing-based computing, especially in the case of large data processing, is usually...