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The study aimed to assess the pathogenicity of the fungus Alternaria alternata on various Tulipa L. species and elucidate its phylogenetic position. The research focused on five specific tulip varieties: T. Albatros, T. Tarda, T. Delta Storm, T. Biflora, and T. Biebersteiniana. Methodologies included molecular analysis, microscopic examinations, cultivation of fungi on PDA, and sequencing of the 18S and 5.8S rRNA genes, as well as the D1/D2 region of the 26S rRNA gene. Results revealed variable pathogenicity across tulip species, with T. Albatros showing complete leaf damage and extensive conidium formation, while T. Biebersteiniana exhibited minimal damage. Factors influencing infection severity included plant variety, conidium formation, and environmental conditions. Sequencing confirmed the fungus's affiliation with the Alternaria genus and highlighted its close relation to other species. The findings underscore the importance of molecular methods for accurate pathogen identification and phylogenetic classification. These results are crucial for developing targeted disease management strategies and enhancing plant resilience in agriculture.The application of the findings is feasible within agriculture to develop resilient varieties and methods for managing the dissemination of A. alternata. Plant diseases involve complex interactions between pathogens and hosts, where fungi like Alternaria alternata disrupt plant physiology through toxin production and enzyme secretion, making effective management crucial

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A bench scale aerobic sequencing batch reactor (SBR) was evaluated in terms of its potential to treat synthetic dairy wastewater. The 2-l plexiglass bioreactor was supplied with oxygen via a fine bubble air diffuser, fed with synthetic dairy wastewater under various operational conditions. To analyze the process, three significant independent variables — influent chemical oxygen demand (COD), mixed liquor volatile suspended solids (MLVSS), and aeration time — were assessed. Three dependent process and quality parameters (as process responses) were also evaluated: total COD removal efficiency, sludge volume index (SVI) and final pH. The experiments were based on a central composite design (CCD) and analyzed using response surface methodology (RSM). The treatment was limited to the following concentration regimes: COD (1000, 3000 and 5000 mg/l), MLVSS (3000, 5000 and 7000 mg/l) and aeration time (2, 10 and 18 h). Maximum COD removal efficiency (of 96.5%) was obtained for an influent with the following characteristics: CODin: 3000 mg/l, MLVSS 5000 mg/l, and aeration time of 18 h. The study demonstrated the capability of aerobic SBRs for high COD removal from dairy industrial wastewater. Easy operation, low cost, and minimal sludge bulking condition were some of advantages of the SBR system as an option for biological treatment of medium-strength industrial wastewater. The present study provides valuable information about relationships between quality and process parameters for different values of operating variables.

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Applying social capital to refurbish urban streets has meant recognizing opportunities and challenges and shaping processes to its sequences over time. The purpose of the present study is to introduce a strategic framework for applying the potentials and values ​​of social capital in environmental improvement and responsible maintenance and social control of street-related sequences. The main question is that how to transform the role of today's street as an element of neighborhood segregation into a linking element of discrete neighborhoods so as to become a showcase for cultural and social interactions. The method of this research is descriptive-analytical which is in three phases: explaining the relevant conceptual framework for entering the research context, applying it to the research context, analyzing and discussing the objective and subjective findings, Qualitative data analysis is done. The measurement tool is a semi-structured questionnaire, using descriptive statistics and inferential statistics performed by SPSS software were used to evaluate criteria and answer research questions. The research context is Imam Khomeini Street and the neighborhoods adjacent to this street. The sample size was 378 using Cochran formula. Indicators used in this study are invitations, neighborhood personality expression on the street edge, transparency and depth to the street edge, and a sense of belonging and responsible environmental behaviors. The results indicate that the items related to the design of the entrances and the continuation of recreational and tourism activities on the edge and the inner texture of the neighborhoods are of greater importance for identifying street sequences.

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Introduction: Hepatitis C virus (HCV) is the major cause of acute and chronic hepatitis, cirrhosis, and hepatocellular carcinoma worldwide. Because of increasing number of infected patients throughout the world, various studies are concentrated on development of high quality diagnostic tests and genotyping in various regions of the world. Methods: In this study, we used RT-PCR to isolate and amplify the core gene sequence of the hepatitis C virus that is very conserved among various genotypes, from an isolate derived from an Iranian patient with chronic hepatitis. Then it was cloned in pUC18 vector and sequenced with universal primers. In order to produce recombinant core protein, the core gene was cloned in PET28A expression vector and the recombinant plasmid was transformed into BL21 (DE3) bacteria. Results and Discussion: The results of sequencing showed that the core gene of the hepatitis C virus from an isolate derived from an Iranian patient with chronic hepatitis has a higher similarity with 1a (96%) and 1b (95%) strains of the virus. This result is similar to those obtained by previous studies. The presence of a 23.5 KD band in SDS-PAGE and Western blot using monoclonal antibody, proved the expression of Core protein in PET28A vector. Mass production of this protein could lead to its use in detection of anti-HCV antibodies in infected patients by immunoassays.

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Backgrounds: This study was conducted with the aim of isolation and molecular identification of Streptomyces spp. producing antibacterial compounds from Iranian soil.
Materials & Methods: In this study, 50 soil samples were collected from different areas of Sanandaj city. Soil samples were cultured on starch casein media. Streptomyces species were characterized using morphological and biochemical assays. Molecular identification was performed by 16S rRNA sequencing. Antimicrobial activity was evaluated using perpendicular streak and agar well diffusion methods.
Findings: To identify active Streptomyces strains in terms of producing antibacterial agents, screening was performed in two stages. Among 20 Streptomyces strains isolated from soil samples, six isolates were selected in the primary screening stage based on their ability to limit the growth of pathogens. Of the two solvents used in the secondary screening stage, ethyl acetate was the most suitable solvent for extracting effective metabolites of Streptomyces. Among the six isolates selected based on their antimicrobial activity, two isolates with the highest antibacterial activity were selected for the sequencing process. By analyzing the dendrogram and the data obtained from the NCBI database, it was found that one isolate (Yellow 4A) was 98% similar to S. fradiae, and the other isolate (Green 4A)  was 98% similar to S. coelicolor.
Conclusion: The use of proper strategies to identify potential new Streptomyces species with antibacterial properties may bring a bright future in the treatment of resistant pathogens. However, more studies are required to detect active metabolites of the mentioned isolates.

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The black pod disease of cocoa in Ghana caused by Phytophthora palmivora and P. megakarya is traditionally managed with fungicides. Because of challenges associated with fungicide use, biological control options, if available, are worth trying. A fungus with proven usefulness in suppressing P. palmivora and P. megakarya in dual plate cultures and cocoa pods has partly been identified as an Aspergillus (designated AI_1). However, its exact identity has been unknown, requiring specific identification by comparing it with known Aspergillus flavus strains (designated AI_2, AI_3, AI_4, and AI_5). It was retested against P. palmivora to confirm the potency of AI_1. The putative A. flavus isolates were also tested for the first time against P. palmivora. Morphological features were determined on carrot agar (CA), potato dextrose agar (PDA), and malt extract agar (MEA). Genomic DNAs from the Aspergillus isolates were subjected to the ITS region and β-tubulin gene sequencing. All the Aspergillus isolates inhibited P. palmivora in assay plates by levels ranging from 89.33 to 95.33% (Experiment 1) and 46.67 to 60.33% (Experiment 2). Generally, the AI_1 produced culture features similar to those of the putative Aspergillus flavus isolates. ITS region sequence analysis grouped all isolates as A. flavus and beta-tubulin also grouped AI_1, AI_2, AI_3, and AI_4 as A. flavus but differentiated AI_5 as A. flavus var. parvisclerotigenus. AI_3 recorded the highest inhibition zone and prevented black pod development of inoculated pods as well. The previously unknown Aspergillus isolates AI_1 is now conclusively identified as A. flavus.

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Objective: Leishmaniasis is caused by parasitic protozoa of the genus Leishmania which in the infected host is obligate intracellular parasite. LACK gene is conserved among related Leishmania species. LACK is the immuno-dominant antigen of L.major which is considered as the most promising molecule for a recombinant or DNA vaccine against leishmaniasis. Materials and Methods: In this study the genomic DNA of an Iranian standard strain of Leishmania major (MRHO/IR/75/ER) was ertracted and the LACK gene was amplilified by PCR. Then the PCR product was cloned into pTZ57R/T cloning vector, The PT-LACK recombinant plasmid was extracted from transformed E.coli bacteria (TG1 strain) and sequenced. Results: The LACK gene (Accession no LmjF28.2740) of MRHO/IR/75/ER & L. major was amplified using PCR method. LACK gene was cloned into pTZ57R/T coloning vector. Sequence analysis of the cloned LACK gene showed high homology 89% with LmjF28.2740 (LACK gene). Conclusion: The LACK gene of L.major was cloned in pTZ57R/T vector successfully. Recombinant plasmid was confirmed and could be used for the production of recomiomort antigens is DNA vaccines, for further studies.

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Objective: Toxoplasmosis, caused by an intracellular protozoan parasite, and the Toxoplasma gondii, is widespread throughout the world. In recent years, significant progress has been made in the identification of vaccine candidates which could induce a protective response. GRA7, an excretory 29 kDa Toxoplasma gondii a dense granular antigen released by infected host cells. In tachyzoite-infected cells, p29 accumulates within the parasitophorous vacuole and co-localizes with its delimiting membrane. Materials and Methods: In the present work, first genomic DNA of Toxoplasma gondii was extracted and used for amplifying of GRA7 gene as a template. Then PCR product was extracted from agarose gel and cloned into TOPO vector. The plasmid containing GRA7 gene was extracted from the transformed bacteria (TOP10 strain) and sequenced. Results: Sequence analysis of GRA7 gene cloned into TOPO vector showed only one base difference when composed with the gene bank sequence for RH strain was only one base. Conclusion: The results indicated that this clone is suitable for subcloning in Prokaryotic and Eukaryotic plasmid.

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The purpose of this study is to investigate those phonological processes, speakers of Persian language and some of Iranian dialects use in order to observe the sonority sequencing principle (SSP) and the syllable contact law (SCL). Among the questions we would like answer the following questions: 1. what phonological processes are used by the speakers of Persian language and some types of Iranian languages in order to observe the sonority sequencing principle and the syllable contact law and 2. What effect does the syllable number of the word have on the application of phonological processes?. Based on the mentioned questions, these hypotheses can be made: 1. the speakers of language use the phonological processes of compensatory lengthening, metathesis, insertion, deletion and substitution in order to observe the sonority sequencing principle and the syllable contact law 2. The syllable number of the simple words does not have any effect on the application of phonological processes.
However, in order to do this research, data of Persian language are collected from the spoken language of the speakers. Then, their phonological forms are compared with Moshiri’s dictionary (2008). Data of Kordi Hurami dialect are gathered through interview with the speakers and data of Lafuri, Torbat Heidariye and Sabzevari dialects are extracted from Kambuziya (2006).
Out of 1125 gathered simple words that do not conform to the SSP and the SCL, the phonological processes of 'compensatory lengthening', 'metathesis', 'insertion', 'deletion' and 'substitution of a phonological unit with another phonological unit' are applied to 357 words by language speakers. In sum, the frequency analysis of data shows that:
The deletion of the glottal consonants / ʔ / and  / h / is more frequent in the two syllable words. In other words, this process occurs in 66/19 percent of disyllabic words, 23/94 percent of tri syllabic words and 9/85 percent of one syllable words. Furthermore, the constraint hierarchy for the phonological process of deletion of the glottal consonants and the compensatory lengthening of a vowel can be illustrated as: SON-SEQ>> No cluster-glottal, MAX-μ >> MAX-IO.
The phonological process of metathesis is more frequent in the disyllabic words. This process occurs in 65/74 percent of two syllable words, 25 percent of monosyllabic words and 9/25 percent of three syllable words. In addition, the constraint hierarchy for the application of metathesis can be shown as: SON-SEQ>> LINEARITY and  SCL>> LINEARITY.
The process of insertion is more frequent in the disyllabicwords. This process occurs in 96/87 percent of disyllabic words and in 3/12 percent of monosyllabic words. The constraint hierarchy of this process can be indicated as: SON-SEQ>> DEP-IO.
An investigation of the extracted Persian simple words shows that the sonority sequencing principle is not observed in 24 words with the structure of /CVC1C2 / . In these cases, the process of deletion is not applied. When the speakers use these monosyllabic simple words in combination with other linguistic elements, the deletion of the final consonant occurs. However, the constraint hierarchy of this process can be illustrated as: SON-SEQ>> MAX-IO.
The process of substitution occurs in some words of kordi Hurami dialect. In other words, when the sonority sequencing principle is not observed in the initial consonant cluster, the second member of the cluster which is less sonorant than the first member is substituted with another consonant which is more sonorant than the first member. The constraint hierarchy of this phonological process can be shown as: SON-SEQ>> *STOP/#C >> IDENT (manner).
Thus, it can be argued that these processes are applied to mono, di and tri syllabic words among which the frequency of disyllabic words is more than that of one and tri syllabic words.

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In Persian, the only syllable type with consonant clusters is cvcc, where its coda can be filled with two consonants. The present article attempts to find whether these two consonant conform the sonority sequencing principle or not. For this reason, the Persian words with cvcc syllable type are gathered from Persian dictionaries and are classified based on the vowel filling the nucleus of the syllables and the consonants in the first or second slot of the coda and the following results were obtained: a. Sonority sequencing principle is confirmed in clusters nuclei are /i,u,a/. b. Sonority sequencing principle is rejected in clusters with vowels /æ, e,o/. c. Based on sonority sequencing principle, vowels in Persian make up two natural classes namely / æ, e,o/ and /i,u,a/.

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Introduction: Proteases are the most important industrial enzymes. Bacillus bacteria are commonly used to produce these enzymes. The aim of this study was cloning, sequencing, expression and bioinformatics study of aprX serine protease gene extracted from Bacillus licheniformis.
Materials and Methods: In this study, after extraction of bacterial DNA, aprX serine protease genes was isolated from Bacillus licheniformis and cloned into pTG19-T vector and then subcloned in pET28a vector. The molecular structure, its biochemical and phylogenetic properties were investigated and three-dimensional structure of the cloned enzyme was predicted. For the induction of gene expression and protein production of the recombinant serine protease IPTG was used at different concentrations, different temperatures and different time periods. Confirmation of aprX gene expression was performed by SDS-PAGE and dot blot analysis. Then, the activity of recombinant protease enzyme was measured at different temperatures and pHs.
Results: Cloning was confirmed by sequencing. Based on the results of phylogenetic studies, the obtained protein sequence showed a high similarity to the sequences of other Bacillus species. After evaluating the drawn models, it was found that the models provided by RAPTROX and I-TASSER software were desirable models for predicting the three dimentional structure of this protease. The recombinant protein production was successfully induced by IPTG induction in the host containing the plasmid pET28a-aprX. The highest expression values were obtained at 25 ° C for 20 hours with 0/5 mM IPTG. Also, the recombinant protein produced showed the highest activity at 50 ° C and pH 8.

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Botrytis cinerea is one of the most important harmful fungi affecting agricultural products. This study focused on the expression changes of Arabidopsis thaliana infected with this fungus. The expression dataset of a microarray and two RNA-sequencing were integrated using the respective software. The list of differentially expressed genes was extracted, and the key genes with altered expression were identified through Cytoscape software. These key genes co-expression patterns and functional enrichment were analyzed. Subsequently, microRNAs and transcription factors associated with these genes were predicted. Ten genes, including GAPA-2, SBPASE, CRB, HCEF1, CaS, ATPD, LIL3:1, PSAH2, PRK, and PMDH2, were identified as crucial down-regulated genes. Additionally, ten genes, namely WRKY33, CZF1, SZF1, STZ, ERF11, RHL41, BAP1, AT1G07135, CMPG2, and TET8, were highlighted as key up-regulated genes. The key roles of the hub genes with a decreased expression included processes and pathways associated with the reductive pentose phosphate cycle, photosynthesis, cold response, fructose and sucrose metabolism, defense response against bacteria, and gluconeogenesis. The key over-expressed genes played important roles in responding to chitin, oxygen deprivation, temperature fluctuations, injuries, fungal attacks, and gene transcription functions. Key genes were associated with ath-miR850, ath-miR393a-5p, and ath-miR393b-5p. Transcription factor SPL7 was linked to the transcription of down-regulated key genes, while transcription factors SARD1, PIF5, CAMTA1, HY5, WRKY33, TOC1, CAMTA3, CAMTA2, BZR1, FAR1, and CAMTA5 were also predicted to be associated with up-regulated genes. Some of these results have not previously been reported. Therefore, they could be used to design practical experiments exploring the interaction between plants and pathogenic fungi.
 

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Objective: Group A rotaviruses (GARV) are responsible for the vast majority of severe diarrhea worldwide that kills an estimated 600,000-870,000 children annually. Since infantile gastroenteritis is a main health problem, therefore diagnosis and treatment of this disease is crucial. Gene rearrangements have been detected in vitro during serial passages of the virus at a high multiplicity of infection (MOI) in cell culture, as well as in chronically infected immunodeficient individuals. In this study, we developed an RT-PCR method to detect and diagnose the standard and gene rearranged bovine rotavirus. Methods: Rotavirus RNA was extracted from confluent monolayers of infected MA-104 cells, stained with silver nitrate, and then electrophoresed in a 10% polyacrylamide gel. The full-length gene products that encoded the NSP1, 2, and 3 genes of the standard and rearranged rotavirus were amplified by RT-PCR using specific primers. Results: We observed rearranged NSP1 and NSP3 genes that had different migration patterns seen with polyacrylamide gel electrophoresis. NSP1, 2, and 3 gene segments from standard and rearranged rotaviruses were amplified by RT-PCR, then the complete nucleotide sequence of each gene was subjected to sequencing. The results showed the generation of gene rearrangement through serial passages of the bovine rotavirus RF strain. Conclusion: Serial passage of rotavirus in cell culture at a high MOI and chronic infection in immunodeficient target groups might alter rotavirus evolution. The methods utilized for detection and characterization of rotaviruses are continually evolving and being refined. Data collection is necessary to understand the molecular and antigenic features of the rotavirus in order to have a successful implementation of rotavirus studies and the development of a rotavirus vaccine. This study shows the importance of genetic variation and can provide valuable information about the amplification, diversity, biology, and evolution of rotaviruses.

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The aim of this study was to evaluate the performances of methods such as sequencing of the internal transcribed spacer (ITS) and 26S (D1/D2) regions of ribosomal DNA, RFLP analysis of the ITS region and commercial biochemical test kit for the identification of the yeasts isolated during spontaneous fermentation of fresh crushed pineapple juice. The experiments were conducted in Thailand and Australia. The yeast isolates in Thailand were identified by sequencing the ITS and 26S (D1/D2) regions of ribosomal DNA and RFLP analysis of the ITS region. The yeast isolates in Australia were identified by sequencing analysis of the two DNA regions and commercial biochemical test kit. The identification results conducted in both countries were relatively similar. Mainly, the yeast isolates could be identified by the use of 26S rDNA in combination with ITS sequencing analysis. In Thailand, approximately 80% of the yeast isolates identified by sequencing analysis of the two regions gave similar identities and included Rhodotolula mucilaginosa, Issatchenkia orientalis, Hanseniaspora uvarum, Hanseniaspora opuntiae, Pichia guilliermondii, Aureobasidium pullulans, Saccharomycodes ludwigii, Candida tropicalis, Pichia fermentans, Zygosaccharomyces bailii, Candida stellata and Erythrobasidium hasegawianum.In Australia, 86% of the yeast isolates gave similar identifications by the sequencing analysis of the two regions and included P. guilliermondii, Pichia membranifaciens, P. fermentans, H. uvarum, H. opuntiae, I. orientalis, Candida sp., Yarrowia lipolytica, Tremella globispora, R. mucilaginosa and A. pullulans.

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Computer-aided process planning (CAPP) is a bridge for integrating computer-aided design (CAD) and computer-aided manufacturing (CAM). One of the basic computer-aided process planning tasks is sequencing of machining features. Sequencing of machining features is determined based on technical and geometrical rules. In this paper, the technical rules, geometrical rules and sequencing of machining features method were discussed. At first, some of the technical rules were pointed. Then, the geometrical interactions were studied and two new geometrical rules were introduced for sequencing the machining features having geometrical interaction. These rules can yield unique results and they are identified easily by the computer systems. Also, an algorithm was introduced for automated application of these geometrical rules in computer systems. The conflict between the technical and geometrical rules that may occur in some cases was studied. This conflict must be considered in the sequencing of machining features methods. Finally, an algorithm was introduced for sequencing of machining features based on permutation. In this algorithm the technical and geometric rules were applied separately and step by step. If there is any conflict between technical and geometrical rules, this conflict could detect automatically in this algorithm. Algorithms were programmed and verified in PythonOCC.

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A total of 58 bacteria from three fermented vegetables samples were isolated. These isolates were identified as 64% Lactobacillus, 5% Pediococcus, 4.5% Leuconostoc and 26.5% unclassified bacteria based on phenotypic characterizations using morphological and biochemical tests. This identification was completed by culture-independent molecular method based on next-generation sequencing of 16S ribosomal RNA gene amplicons. The V3 and V4 regions of 16S rRNA gene were amplified and sequenced using Illumina MiSeq platform. These data were analyzed with BaseSpace software and Greengenes database. The analysis revealed 77.12% Lactobacillus, 7.51% Pediococcus, 5.61% Leuconostoc, 1.20% Acinetobacter, 1.00% Enterobacter, 0.35% Erwinia, 0.35% Dickeya as the predominant genera and 2.79% unclassified bacteria. At species level, 19.32% Lactobacillus brevis, 15.71% Lactobacillus japonicus, 13.25% Lactobacillus pentosus, 10.26% Lactobacillus senmaizukei, 4.6% Lactobacillus plantarum, 2.65% Leuconostoc mesenteroides and 2.32% Lactobacillus acidifarinae and 17.26% unclassified bacteria were identified. The same identification results were obtained by both phenotypic and Next- generation sequencing assays at genus level. In this study, application of next generation sequencing in identification of whole microbial community of this fermented product revealed that lactic acid bacteria include Lactobacillus, Pediococcus and Leuconostoc as dominant flora, were involved in fermentation process. Non-lactic acid bacteria such as Acinetobacter, Enterobacter, Erwinia and Dickeya genera also play important role in fermented pickled vegetable with tomato juice ripening. Moreover, probiotic bacteria such as Lactobacillus plantarum, Lactobacillus pentosus, Leuconostoc mesenteroides and Lactobacillus brevis were identified in this fermented product.

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DNA sequence determination is a tremendous human achievement. DNA sequencing includes several methods and technologies in use for determining the order of the nucleotide bases (adenine, guanine, cytosine, and thymine) in a molecule of DNA. Knowledge of DNA sequences has become indispensable for basic biological research, other research branches utilizing DNA sequencing, and in numerous applied fields such as diagnostic, biotechnology, forensic biology and biological systematics. The advent of DNA sequencing has significantly accelerated biological research and discovery. Rapid sequencing, the result of modern DNA sequencing technology, is instrumental in the sequencing of the human genome for the Human Genome Project. Related projects, often by scientific collaboration across continents, have generated complete DNA sequences of humans as well as numerous animals, plants and microbial genomes. DNA sequencing methods currently under development include labeling DNA polymerase and reading the sequence as a DNA strand transits through nanopores. Additional methods include microscopy-based techniques such as atomic force microscopy or transmission electron microscopy that are used to identify the positions of individual nucleotides within long DNA fragments (>5000 bp) by nucleotide labeling with heavier elements (e.g., halogens) for visual detection and recording. Third generation technologies aim to increase throughput and decrease the time to result and cost by eliminating the need for excessive reagents and harnessing the processivity of DNA polymerase. Researchers in the field of genetics in Iran use this technology in their studies, but unfortunately our literature lack proper Persian language resources. The authors intend to write a series of review articles in this field. The present paper is an introduction to the summary of important techniques in DNA sequencing.

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DNA is made up of molecules called nucleotides. There are four different nucleotides in DNA which are called Adenine, Guanine, Cytosine, and Thymine, or simply A, G, C and T. Determining the order of these bases is called DNA sequencing. This sequence determines the genes and these genes specify an individual’s unique traits. Therefore, the genetic research plays an important role in detection, prevention and treatment of diseases which are caused by genetic abnormalities and mutations. Common DNA sequencing methods are usually based on chemical reactions. These methods have some disadvantages for example they are expensive and also they cause losing DNA. So, in recent years the progress in molecular scale simulation methods has made various approaches for DNA sequencing. In this paper, a suitable method for DNA sequencing has been presented and its accuracy is investigated by molecular dynamics simulations. In this method, DNA molecule passes through the carbon nanotube first, and then the graphene nanopore, with a specific speed. Different bases are determined by analyzing the required force for passing DNA. In this proposed method, the speed and cost of sequencing are improved.