Assembly Program Research Articles

Hidden Markov Model Based Graph Construction Process for DNA Sequence Assembly

Through using next-generation sequencers to decode DNA symbols has been a majorly breakthrough in the area of genomic research for decades. A plenty of current approaches of next-generation sequencers with high throughput rates as well as relatively low costs, but it is still challenged for the assembly of the reads which those sequencers produces. We proposed, in this paper, a novel Hidden Markov Model based (HMM-based) approach for next-generation genome sequence assembly programs. The paper introduces the major challenges that currently existed assemblers encounter in the next-generation environment, and four basic stages included in our proposed method: a) pre-processing filtering, b) a graph construction process, c) a graph simplification process, d) post-processing filtering. Experimental results prove the performance of the new approach meets or exceeds the state-of-art by testing a number of DNA open-source datasets.

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences.

In metagenomic studies of microbial communities, the short reads come from mixtures of genomes. Read assembly is usually an essential first step for the follow-up studies in metagenomic research. Understanding the power and limitations of various read assembly programs in practice is important for researchers to choose which programs to use in their investigations. Many studies evaluating different assembly programs used either simulated metagenomes or real metagenomes with unknown genome compositions. However, the simulated datasets may not reflect the real complexities of metagenomic samples and the estimated assembly accuracy could be misleading due to the unknown genomes in real metagenomes. Therefore, hybrid strategies are required to evaluate the various read assemblers for metagenomic studies. In this paper, we benchmark the metagenomic read assemblers by mixing reads from real metagenomic datasets with reads from known genomes and evaluating the integrity, contiguity and accuracy of the assembly using the reads from the known genomes. We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and Faucet, for evaluation. We showed the strengths and weaknesses of these assemblers in terms of integrity, contiguity and accuracy for different variables, including the genetic difference of the real genomes with the genome sequences in the real metagenomic datasets and the sequencing depth of the simulated datasets. Overall, MetaSPAdes performs best in terms of integrity and continuity at the species-level, followed by MEGAHIT. Faucet performs best in terms of accuracy at the cost of worst integrity and continuity, especially at low sequencing depth. MEGAHIT has the highest genome fractions at the strain-level and MetaSPAdes has the overall best performance at the strain-level. MEGAHIT is the most efficient in our experiments. Availability: The source code is available at https://github.com/ziyewang/MetaAssemblyEval.

Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)

BackgroundDe novo assembling of large genomes, such as in conifers (~ 12–30 Gbp), which also consist of ~ 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computing limitations of nucleotide sequence assembly programs (DNA assemblers). As a rule, modern assemblers are usually designed to assemble genomes with a length not exceeding the length of the human genome (3.24 Gbp). Most assemblers cannot handle the amount of input sequence data required to provide sufficient coverage needed for a high-quality assembly.ResultsAn original stepwise method of de novo assembly by parts (sets), which allows to bypass the limitations of modern assemblers associated with a huge amount of data being processed, is presented in this paper. The results of numerical assembling experiments conducted using the model plant Arabidopsis thaliana, Prunus persica (peach) and four most popular assemblers, ABySS, SOAPdenovo, SPAdes, and CLC Assembly Cell, showed the validity and effectiveness of the proposed stepwise assembling method.ConclusionUsing the new stepwise de novo assembling method presented in the paper, the genome of Siberian larch, Larix sibirica Ledeb. (12.34 Gbp) was completely assembled de novo by the CLC Assembly Cell assembler. It is the first genome assembly for larch species in addition to only five other conifer genomes sequenced and assembled for Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana, and Pseudotsuga menziesii var. menziesii.

Choice of assembly software has a critical impact on virome characterisation

BackgroundThe viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets.DesignThis study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely, simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes.ResultsAssembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low-accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.

The Evolution of Centriole Structure: Heterochrony, Neoteny, and Hypermorphosis.

Centrioles are subcellular organelles that were present in the last eukaryotic common ancestor, where the centriole's ancestral role was to form cilia. Centrioles have maintained a remarkably conserved structure in eukaryotes that have cilia, while groups that lack cilia have lost their centrioles, highlighting the structure-function relationship that exists between the centriole and the cilium. In contrast, animal sperm cells, a ciliated cell, exhibit remarkable structural diversity in the centriole. Understanding how this structural diversity evolved may provide insight into centriole assembly and function, as well as their unique role in sperm. Here, we apply concepts used in the study of the evolution of animal morphology to gain insight into the evolution of centriole structure. We propose that centrioles with an atypical structure form because of changes in the timing of centriole assembly events, which can be described as centriolar "heterochrony." Atypical centrioles of insects and mammals appear to have evolved through different types of heterochrony. Here, we discuss two particular types of heterochrony: neoteny and hypermorphosis. The centriole assembly of insect sperm cells exhibits the retention of "juvenile" centriole structure, which can be described as centriolar "neoteny." Mammalian sperm cells have an extended centriole assembly program through the addition of novel steps such as centrosome reduction and centriole remodeling to form atypical centrioles, a form of centriole "hypermorphosis." Overall, centriole heterochrony appears to be a common mechanism for the development of the atypical centriole during the evolution of centriole assembly of various animals' sperm.

A Verification Framework for Assembly Programs Under Relaxed Memory Model Using SMT Solver

A Verification Framework for Assembly Programs Under Relaxed Memory Model Using SMT Solver

Transcriptome analysis of Sclerotinia ginseng and comparative analysis with the genome of Sclerotinia sclerotiorum

Sclerotinia ginseng is a non-model necrotrophic pathogen responsible for a serious epidemic in the ginseng production area in northeast China. In this study, de novo RNA sequencing was carried out using an Illumina HiSeq™ 4000 platform in conjunction with the short-read assembly program Trinity. The S. ginseng transcriptome was compared with that of Sclerotinia sclerotiorum, and species-specific unigenes were annotated with KEGG and GO terms. Phylogenetic analysis of amino acid sequences for four polygalacturonase (pg) genes and a pH-response transcription factor (pac1) homologous gene identified in S. ginseng revealed a close evolutionary relationship with other species of Sclerotiniaceae.

A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes.

BackgroundSillaginidae, also known as smelt-whitings, is a family of benthic coastal marine fishes in the Indo-West Pacific that have high ecological and economic importance. Many Sillaginidae species, including the Chinese sillago (Sillago sinica), have been recently described in China, providing valuable material to analyze genetic diversification of the family Sillaginidae. Here, we constructed a reference genome for the Chinese sillago, with the aim to set up a platform for comparative analysis of all species in this family.FindingsUsing the single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) Sequel, we generated ∼27.3 Gb genomic DNA sequences for the Chinese sillago. We reconstructed a genome assembly of 534 Mb using a strategy that takes advantage of complementary strengths of two genome assembly programs, Canu and FALCON. The genome size was consistent with the estimated genome size based on k-mer analysis. The assembled genome consisted of 802 contigs with a contig N50 length of 2.6 Mb. We annotated 22,122 protein-coding genes in the Chinese sillago genomes using a de novo method as well as RNA sequencing data and homologies to other teleosts. According to the phylogenetic analysis using protein-coding genes, the Chinese sillago is closely related to Larimichthys crocea and Dicentrarchus labrax and diverged from their ancestor around 69.5–82.6 million years ago.ConclusionsUsing long reads generated with PacBio sequencing technology, we have built a draft genome assembly for the Chinese sillago, which is the first reference genome for Sillaginidae species. This genome assembly sets a stage for comparative analysis of the diversification and adaptation of fishes in Sillaginidae.

Development of an Automatic Mini-Conveyor System for Product Monitoring

This thesis presents the development of an automatic mini-conveyor system for product monitoring. It is aimed at solving relative industrial and manufacturing problems such as product pilferage, inefficient supervision, monitoring and workmanship. It is also to improve production management system, using ICT based platform to enhance monitoring control and data acquisition (MCDA) system in manufacturing process. ASSEMBLY programming language was used on a programmable logic controller (Atmel 89C52) microcontroller for control and monitoring protocol. The method includes; simulation, hardware development; to include; sensing, counting and signalling wireless system containing sensors and a wireless radio frequency transmitter and receiver. Design calculation analysis, fabrication and operational tests were carried out on the developed mini-conveyor. The operational and test result shows that, the time the product travels along the conveyor through a distance of 0.8m between entrance and exit point sensors was between 15.7sec to 16.3sec. At a distance of 0.096metres between sensors, the response to display time on LCD is approximately 1.0 second. The developed mini-conveyor system is able to remotely monitor a product on a communication distance of 22 metres in which the required information is displayed on computer screen on a telnet hyper-terminal platform, through a baud rate of 1200. Therefore, the developed machine has open opportunities for product monitoring control and data acquisition in material handling systems in the industries for more accountability.

Application for Emu8086 and Proteus in Microcomputer Principle Teaching

Combined with the teaching of Microcomputer Principle and interface technology in electrical engineering and automation, the authors proposes a new teaching method. Firstly, the authors analyzed the teaching and learning situation of Microcomputer Principle and interface technology. Secondly, in the theory and practice teaching process, the authors put forward a new designing scheme that through the Emu8086 and Proteus software for assembly program writing, hardware circuit design and simulation design. The simulation example of frequency divider circuit is constructed by 8086 and 8253A.The experimental results show that the constructed frequency divider circuit can be realized by 8086 simulation. Finally, the authors summarizes the teaching methods of virtual simulation for Emu8086 and Proteus software, and obtains very good teaching results. In this paper, this innovation mode(that is, through the vivid simulation effect) arouse the student's study enthusiasm and provides a new method for embedded curriculum teaching reform.

A practical microwatt-meter for electrical energy measurement in programmable devices

Background: In this work, an accurate low-cost power microwatt-meter is designed, built, and tested. This microwatt-meter is found to be capable of measuring power consumption in a wide range of devices and sensors, such as nodes in wireless sensor networks, microcontrollers in Internet of Things devices, and Field Programmable Gate Arrays. Methods: The paper examines the usage of the microwatt-meter for the measurement of power consumption in digital devices as they execute program instructions, ranging from a low-level single step (instruction) in an assembly program to a high-level sophisticated program or system. Results: The results obtained showed that the microwatt-meter is highly accurate. It can measure the energy consumed by any of the devices/programs/instructions in a digital system with accuracy levels ranging between 0.5% and 2.5% (depending on the application). Conclusion: The accuracy of the microwatt-meter is validated using the fundamental conservation of energy law and a comparison with multimeter current measurements is presented.

Configurable simulator for computer architecture and organization

AbstractThis paper presents a novel visual educational configurable simulator for computer architecture and organization (COCONUT). By using the simulator students can create their own processor with an arbitrary architecture and simple organization on the register transfer level, write an assembly program to be executed on the processor and observe the instruction execution phases of the program on the processor. The students can create their processor by using the simulator of a computer system with fixed and configurable parts. The configurable part allows students to use the simulator for defining the instruction decoding of the processor operation unit and the content of the microprogram memory of the processor control unit. The simulator's usage was evaluated at the University of Belgrade—School of Electrical Engineering on two courses for two consecutive school years. The evaluation results showed that 80% of the students stated that the simulator helped them to better understand the course material and that they had a positive user experience with the simulator.

An assessment of stakeholder participation in monitoring and evaluation of district assembly projects and programmes in the Savelugu-Nanton Municipality Assembly, Ghana

Participatory Monitoring and Evaluation (PM&E) of projects and programmes promotes greater transparency and accountability in development governance. Some studies revealed that participation in Metropolitan, Municipal and District Assemblies in monitoring and evaluation (M&E) is low. This study adopted a case study approach. A sample of 196 people participated in the study. The study revealed that stakeholder participation in M&E of projects and programmes was high among the Municipal Planning and Co-ordinating Unit (MPCU) members and the District Assembly members but low at the Zonal Council and community levels. This has impacted negatively on the transparency, accountability and the sustenance of projects and programmes. The study concludes that stakeholders were rarely involved in M&E of projects and programmes due to lack of concerted effort by the MPCU for grass root stakeholder participation and poor attitude on the part of community level stakeholders in M&E of projects and programmes. The MPCU and the Assembly members’ involvement were appreciably high whereas the Unit committee, the community and the Zonal councils’ involvement were low. The study recommends that the District Assembly through the MPCU should establish strategies such as increased engagement of the substructures in the planning, implementation, monitoring and evaluation process, creating an enabling environment for the substructures to set their own targets, support them to meet the targets and build their capacities to report regularly to communities under them and to the Municipal Assembly. The Municipal Assembly should partner with the Sub-structures to embark on community sensitization on participatory monitoring and evaluation of projects and programmes.Keywords: Participatory Monitoring and Evaluation, Stakeholders, Community Participation, Projects, Programmes, Savelugu-Nanton

Fault Attacks Made Easy: Differential Fault Analysis Automation on Assembly Code

Over the past decades, fault injection attacks have been extensively studied due to their capability to efficiently break cryptographic implementations. Fault injection attack models are normally determined by analyzing the cipher structure and finding exploitable spots in non-linear and permutation layers. However, this level of abstraction is often too high to distinguish vulnerable parts of software implementations, due to specific operations and optimizations. On the other hand, manually analyzing the assembly code requires non-negligible amount of time and expertise. In this paper, we propose an automated approach for analyzing cipher implementations in assembly. We represent the whole assembly program as a data flow graph so that the vulnerable spots can be found efficiently. Fault propagation is analyzed in a subgraph constructed from each vulnerable spot, allowing equations for Differential Fault Analysis (DFA) to be automatically generated. We have created a tool that implements our approach: DATAC – DFA Automation Tool for Assembly Code. We have successfully used this tool for attacking PRESENT- 80, being able to find implementation-specific vulnerabilities that can be exploited in order to recover the last round key with 16 faults. Our results show that DATAC is useful in finding attack spots that are not visible from the cipher structure, but can be easily exploited when dealing with real-world implementations.

Using Bacterial Transcriptomics to Investigate Targets of Host‐Bacterial Interactions in C. elegans

The interactions between a host and its resident microbes form complicated networks and disentangling these interactions can help us better understand mechanisms of pathogenesis while also defining the integral commensal protection that host‐associated microbiota offer to promote health. Here we utilize a tractable model organism, C. elegans, to study the mechanisms involved in host‐microbe interactions and to identify different expression profiles under different host genotypes to increase our knowledge of host‐bacteria interspecies interactions. We developed an RNAseq protocol and bioinformatics pipeline to elucidate 1) bacterial gene expression differences in host associated versus in vitro E. coli OP50 and 2) differential bacterial gene expression in known models of aging within C. elegans (long‐lived daf‐2/InsR mutant versus short‐lived daf‐16/FOXO transcription factor mutant). Briefly, RNA extracts (n=18) were subject to ribosomal RNA subtraction, cDNA synthesis, Nextera library preparation and sequencing using the Illumina Hiseq platform. Our bioinformatics pipeline utilizes the most robust programs for quality filtering, assembly, annotation, and differential gene analysis. Our analysis revealed a variety of differentially expressed genes in plated E. coli OP50 versus E. coli OP50 fed to C. elegans. Differential gene expression analysis revealed that expression of biosynthetic genes was enriched in host‐associated E. coli, and several of these expressed genes code for the precursors and products needed for the synthesis of Lipopolysaccharides (LPS), which are important in innate immune and stress responses, as well as pathogenicity. Preliminary bacterial transcriptome data also indicate differences in bacterial expression of several biosynthetic pathways and virulence mechanisms, which may contribute to the aging phenotypes of the long‐lived daf‐2/InsR mutant and the short‐lived daf‐16/FOXO transcription factor mutant. Our research has employed a robust RNA sequencing and bioinformatics approach to study differential gene expression of bacteria in C. elegans, and will enable us to better test how gut bacteria and their gene regulatory networks regulate host physiology.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Automatic translation of assembly shellcodes to printable byte codes

The generation of printable shellcode is an important computer security research area. The original idea of the printable shellcode generation was to write a binary, executable code in a way that the generated byte code contains only bytes that are represented by the English letters, numbers and punctuation characters. In this way unfortunately only a limited number of CPU instructions can be used. In the originally published paper a small decoder is written with instructions represented by printable characters and the shellcode is decoded on the stack to be executed later. This paper, however describes a proof of concept project, which converts the source code of a full assembly program or shellcode to a new source code, whose compiled binary code contains only printable characters. The paper also presents new, printable character implementation of some CPU instructions.

A hybrid simulation platform for learning microprocessors

AbstractModern engineering applications are based on microprocessors and microcontrollers. Thus, the microprocessor (uP) architecture constitutes a core course component in engineering education. Many technologies have been used by the Universities in the past 30 years for learning uPs. In the 1980s, hardware platforms have been used (e.g., MPF‐I) for learning assembly programming in hexadecimal mode of popular microprocessor models. The above platforms have been replaced by software simulators where the uP components are represented by visual objects. The software based approaches have lack of uP architecture customization and are limited only in assembly programming. On the other hand, the existing hardware based tools are low level and very complicated. Thus, the students do not work on uP design and assembly language development. In this paper, a novel hybrid simulator platform which changes the educational point of view regarding the uP learning methodology is presented. The proposed hybrid simulation platform (HSP) consists of hardware components which represent the uP architectural units and software components for system operation and administration. Using the HSP, students freely select the uP hardware based components and build their own architecture. On the other hand, professors can create educational scenarios with customizable experimental architectures.

Tecnologias de informação e comunicação no compartilhamento de aprendizagens na educação básica

The purpose of this article is to investigate both digital and non-digital technologies used to promote the sharing of learning experiences in learning through research in Basic Education. For such, a qualitative approach was followed, with data being gathered through a semistructured interview with seven Basic Education teachers working in different areas (History, Pedagogy, Computing and Geography) in both public and private schools in the Vale do Taquari/RS/BRA region. Moreover, the individuals involved are undergraduate Master Degree at the Post-Graduation Teaching Program at a Higher Education Institution. Content analysis was used to analyze the gathered data. The theoretical foundation used for this study is based on the teaching through research presumptions and in the relation between technology and pedagogical practices. The collected data allowed for the construction of two analysis categories: a) learning experiences shared through immaterial technological resources; b) learning experiences shared through material technological resources. The results point towards the importance of producing posters and panels, as well as using the digital board, the Internet, game assembly programs and animations together with the teaching and learning processes in Basic Education.

IsoTree: A New Framework for de novo Transcriptome Assembly from RNA-seq Reads.

High-throughput sequencing of mRNA has made the deep and efficient probing of transcriptome more affordable. However, the vast amounts of short RNA-seq reads make de novo transcriptome assembly an algorithmic challenge. In this work, we present IsoTree, a novel framework for transcripts reconstruction in the absence of reference genomes. Unlike most of de novo assembly methods that build de Bruijn graph or splicing graph by connecting k- mers which are sets of overlapping substrings generated from reads, IsoTree constructs splicing graph by connecting reads directly. For each splicing graph, IsoTree applies an iterative scheme of mixed integer linear program to build a prefix tree, called isoform tree. Each path from the root node of the isoform tree to a leaf node represents a plausible transcript candidate which will be pruned based on the information of paired-end reads. Experiments showed that in most cases IsoTree performs better than other leading transcriptome assembly programs. IsoTree is available at https://github.com/Jane110111107/IsoTree.

Modelling reversible execution of robotic assembly

SUMMARYProgramming robotic assembly for industrial small-batch production is challenging; hence, it is vital to increase robustness and reduce development effort in order to achieve flexible robotic automation. A human who has made an assembly error will often simply undo the process until the error is undone and then restart the assembly. Conceptually, robots could do the same. This paper introduces a programming model that enables robot assembly programs to be executed in reverse. We investigate the challenges in running robot programs backwards and present a classification of reversibility characteristics. We demonstrate how temporarily switching the direction of program execution can be an efficient error recovery mechanism. Moreover, we demonstrate additional benefits arising from supporting reversibility in an assembly language, such as increased code reuse and automatically derived disassembly sequences. As a default approach to reversibility, we use program inversion and statement-level inversion of commands, but with a novel override option providing alternative sequences for asymmetric reverse actions. To efficiently program for this model, this paper introduces a new domain-specific language, SCP-RASQ (Simple C++ Reversible Assembly SeQuences). In initial experiments, where 200 consecutive assemblies of two industrial cases were performed, 18 of 22 errors were corrected automatically using only the trial-and-error capabilities that come from reverse execution.