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phylogenetics
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Fast Alignment-free Protein Comparison Approach based on FPGA Implementation
, M.Sc. Thesis Sharif University of Technology ; Koohi, Somayyeh (Supervisor)
Abstract
Protein, as the functional unit of the cell, plays a vital role in its biological function. With the advent of advanced sequencing techniques in recent years and the consequent exponential growth of the number of protein sequences extracted from diverse biological samples, their analysis, comparison, and classification have faced a considerable challenge. Existing methods for comparing proteins divide into two categories: methods based on alignment and alignment-free. Although alignment-based methods are among the most accurate methods, they face inherent limitations such as poor analysis of protein groups with low sequence similarity, time complexity, computational complexity, and memory...
HLA alleles and haplotype frequencies in Iranian population
, Article Human Antibodies ; Volume 30, Issue 2 , 2022 , Pages 79-96 ; 10932607 (ISSN) ; Hussen, B. M ; Pashmforoush, S ; Akbari, M. T ; Arsang-Jang, S ; Nazer, N ; Hamidieh, A. A ; Hajifathali, A ; Dinger, M. E ; Sayad, A ; Dehaghi, M. O ; Sharif University of Technology
IOS Press BV
2022
Abstract
BACKGROUND: HLA genotyping is a prerequisite for selection of suitable donors in the process of bone marrow transplantation. METHODS: In the current study, the frequencies of HLA-A, -B, -C and -DRB1 alleles and A-B-C-DRB1 haplotypes were assessed in 855 healthy Iranian persons using a low-resolution sequence specific primer (SSP) kit. RESULTS: Frequencies were compared between 11 subpopulations including Armani, Balouch, Bandari, Turk, Turkaman, Arab, Fars, Kurd, Gilaki, Lor and Mazani. In total, 17 HLA-A alleles were detected, one of which (HLA-A*74) was present only among Lors. HLA-A*23 and -A*26 were the most frequent HLA-A alleles among Armanis. HLA-A*23 was also common among Turkamans....
Efficient biodegradation of naphthalene by a newly characterized indigenous achromobacter sp. FBHYA2 isolated from Tehran oil refinery complex
, Article Water Science and Technology ; Volume 66, Issue 3 , March , 2012 , Pages 594-602 ; 02731223 (ISSN) ; Borghei, S. M ; Hassani, A. H ; Yakhchali, B ; Ardjmand, M ; Zeinali, M ; Sharif University of Technology
IWA Pub
2012
Abstract
A bacterial strain, FBHYA2, capable of degrading naphthalene, was isolated from the American Petroleum Institute (API) separator of the Tehran Oil Refinery Complex (TORC). Strain FBHYA2 was identified as Achromobacter sp. based on physiological and biochemical characteristics and also phylogenetic similarity of 16S rRNA gene sequence. The optimal growth conditions for strain FBHYA2 were pH 6.0, 30°C and 1.0% NaCl. Strain FBHYA2 can utilize naphthalene as the sole source of carbon and energy and was able to degrade naphthalene aerobically very fast, 48 h for 96% removal at 500 mg/L concentration. The physiological response of Achromobacter sp., FBHYA2 to several hydrophobic chemicals...