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Quantification of muscle fiber malformations using edge detection to investigate chronic muscle pressure ulcers. 利用边缘检测对肌纤维畸形进行量化,以研究慢性肌肉压疮。
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-10-21 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1450146
Charlene Z L Ong, N Jannah M Nasir, Roy E Welsch, Lisa Tucker-Kellogg, Jagath C Rajapakse

Background: Microscopy of regenerated tissue shows different morphologies between the healing of acute wounds and chronic wounds. This difference can be seen manually by biologists, but computational methods are needed to automate the characterization of morphology and regenerative quality in regenerated muscle tissue.

Results: From the detected edge segments, we computed several imaging biomarkers of interest, such as median tortuosity, number of edge segments normalized by area, median edge segment distance and interquartile range of orientation angles of edge segments of the microscope images of successful and unsuccessful muscle regeneration. We observed that muscle fibers in saline-treated pressure ulcers had a larger interquartile range of orientation angles of the edge segments (p = 0.05) and shorter edge segment distances (p = 0.003) compared to those of acute cardiotoxin injuries.

Conclusion: Our edge detection method was able to identify statistically significant differences in some of the imaging biomarkers between saline-treated pressure ulcers and cardiotoxin injuries, suggesting that chronic pressure ulcers have increased muscle fiber malformations compared to cardiotoxin injuries.

背景:再生组织的显微镜检查显示,急性伤口愈合与慢性伤口愈合的形态不同。生物学家可以通过手工操作看出这种差异,但需要计算方法来自动表征再生肌肉组织的形态和再生质量:从检测到的边缘片段中,我们计算了几个感兴趣的成像生物标志物,如迂曲度中位数、按面积归一化的边缘片段数量、边缘片段距离中位数以及成功和不成功肌肉再生显微镜图像边缘片段方向角的四分位数间范围。我们观察到,与急性心脏毒素损伤的肌肉纤维相比,生理盐水处理过的压疮肌肉纤维的边缘区段定向角的四分位数间范围更大(p = 0.05),边缘区段距离更短(p = 0.003):结论:我们的边缘检测方法能够发现生理盐水处理过的压疮和心脏毒素损伤之间在某些成像生物标志物上存在统计学意义上的显著差异,这表明与心脏毒素损伤相比,慢性压疮的肌纤维畸形有所增加。
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引用次数: 0
DCMA: faster protein backbone dihedral angle prediction using a dilated convolutional attention-based neural network. DCMA:利用基于注意力的扩张卷积神经网络更快地预测蛋白质骨架二面角。
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-10-18 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1477909
Buzhong Zhang, Meili Zheng, Yuzhou Zhang, Lijun Quan

The dihedral angle of the protein backbone can describe the main structure of the protein, which is of great significance for determining the protein structure. Many computational methods have been proposed to predict this critically important protein structure, including deep learning. However, these heavyweight methods require more computational resources, and the training time becomes intolerable. In this article, we introduce a novel lightweight method, named dilated convolution and multi-head attention (DCMA), that predicts protein backbone torsion dihedral angles ( ϕ , ψ ) . DCMA is stacked by five layers of two hybrid inception blocks and one multi-head attention block (I2A1) module. The hybrid inception blocks consisting of multi-scale convolutional neural networks and dilated convolutional neural networks are designed for capturing local and long-range sequence-based features. The multi-head attention block supplementally strengthens this operation. The proposed DCMA is validated on public critical assessment of protein structure prediction (CASP) benchmark datasets. Experimental results show that DCMA obtains better or comparable generalization performance. Compared to best-so-far methods, which are mostly ensemble models and constructed of recurrent neural networks, DCMA is an individual model that is more lightweight and has a shorter training time. The proposed model could be applied as an alternative method for predicting other protein structural features.

蛋白质骨架的二面角可以描述蛋白质的主要结构,对确定蛋白质结构具有重要意义。为了预测这一至关重要的蛋白质结构,人们提出了许多计算方法,包括深度学习。然而,这些重量级方法需要更多的计算资源,训练时间变得难以忍受。在本文中,我们介绍了一种新颖的轻量级方法,名为扩张卷积和多头注意力(DCMA),可以预测蛋白质骨架扭转二面角(ϕ , ψ)。DCMA 由五层两个混合起始模块和一个多头注意模块 (I2A1) 叠加而成。混合起始块由多尺度卷积神经网络和扩张卷积神经网络组成,旨在捕捉基于序列的局部和长程特征。多头注意力模块补充加强了这一操作。拟议的 DCMA 在公开的蛋白质结构预测关键评估(CASP)基准数据集上进行了验证。实验结果表明,DCMA 获得了更好或相当的泛化性能。迄今为止的最佳方法大多是由递归神经网络构建的集合模型,与之相比,DCMA 是一种单个模型,更轻便,训练时间更短。所提出的模型可作为预测其他蛋白质结构特征的替代方法。
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引用次数: 0
Computational identification and characterization of chitinase 1 and chitinase 2 from neotropical isolates of Beauveria bassiana. 计算鉴定和表征来自新热带贝维氏菌分离物的几丁质酶 1 和几丁质酶 2。
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-10-18 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1434442
Juan Segura-Vega, Allan González-Herrera, Ramón Molina-Bravo, Stefany Solano-González

Background: The fungus Beauveria bassiana is widely used for agronomical applications, mainly in biological control. B. bassiana uses chitinase enzymes to degrade chitin, a major chemical component found in insect exoskeletons and fungal cell walls. However, until recently, genomic information on neotropical isolates, as well as their metabolic and biotechnological potential, has been limited.

Methods: Eight complete B. bassiana genomes of Neotropical origin and three references were studied to identify chitinase genes and its corresponding proteins, which were curated and characterized using manual curation and computational tools. We conducted a computational study to highlight functional differences and similarities for chitinase proteins in these Neotropical isolates.

Results: Eleven chitinase 1 genes were identified, categorized as chitinase 1.1 and chitinase 1.2. Five chitinase 2 genes were identified but presented a higher sequence conservation across all sequences. Interestingly, physicochemical parameters were more similar between chitinase 1.1 and chitinase 2 than between chitinase 1.1 and 1.2.

Conclusion: Chitinases 1 and 2 demonstrated variations, especially within chitinase 1, which presented a potential paralog. These differences were observed in their physical parameters. Additionally, CHIT2 completely lacks a signal peptide. This implies that CHIT1 might be associated with infection processes, while CHIT2 could be involved in morphogenesis and cellular growth. Therefore, our work highlights the importance of computational studies on local isolates, providing valuable resources for further experimental validation. Intrinsic changes within local species can significantly impact our understanding of complex pathogen-host interactions and offer practical applications, such as biological control.

背景:真菌 Beauveria bassiana 被广泛应用于农学领域,主要是生物防治。B. bassiana 利用几丁质酶降解几丁质,几丁质是昆虫外骨骼和真菌细胞壁中的主要化学成分。然而,直到最近,有关新热带分离菌的基因组信息及其代谢和生物技术潜力还很有限:方法:我们研究了 8 个新热带地区的完整 B. bassiana 基因组和 3 个参考文献,以确定几丁质酶基因及其相应的蛋白质,并使用人工整理和计算工具对这些基因组进行了整理和特征描述。我们进行了一项计算研究,以突出这些新热带分离株中几丁质酶蛋白的功能差异和相似性:结果:确定了 11 个几丁质酶 1 基因,分为几丁质酶 1.1 和几丁质酶 1.2。发现了 5 个几丁质酶 2 基因,但在所有序列中呈现出较高的序列保守性。有趣的是,与几丁质酶 1.1 和 1.2 相比,几丁质酶 1.1 和几丁质酶 2 的理化参数更为相似:几丁质酶 1 和 2 显示出了差异,尤其是几丁质酶 1,它是一个潜在的旁系亲属。这些差异体现在它们的物理参数上。此外,CHIT2 完全缺乏信号肽。这意味着 CHIT1 可能与感染过程有关,而 CHIT2 可能参与形态发生和细胞生长。因此,我们的工作凸显了对本地分离物进行计算研究的重要性,为进一步的实验验证提供了宝贵的资源。本地物种的内在变化会极大地影响我们对复杂的病原体-宿主相互作用的理解,并提供实际应用,如生物防治。
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引用次数: 0
Identification of novel drug targets for Helicobacter pylori: structure-based virtual screening of potential inhibitors against DAH7PS protein involved in the shikimate pathway. 幽门螺旋杆菌新型药物靶点的鉴定:基于结构的莽草酸途径DAH7PS蛋白潜在抑制剂虚拟筛选。
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-10-18 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1482338
Narjes Noori Goodarzi, Mahshid Khazani Asforooshani, Behzad Shahbazi, Nayereh Rezaie Rahimi, Farzad Badmasti

Background: Helicobacter pylori, a bacterium associated with severe gastrointestinal diseases and malignancies, poses a significant challenge because of its increasing antibiotic resistance rates. This study aimed to identify potential drug targets and inhibitors against H. pylori using a structure-based virtual screening (SBVS) approach.

Methods: Core-proteome analysis of 132 H. pylori genomes was performed using the EDGAR database. Essential genes were identified and human and gut microbiota homolog proteins were excluded. The DAH7PS protein involved in the shikimate pathway was selected for the structure-based virtual screening (SBVS) approach. The tertiary structure of the protein was predicted through homology modeling (based on PDB ID: 5UXM). Molecular docking was performed to identify potential inhibitors of DAH7PS among StreptomeDB compounds using the AutoDock Vina tool. Molecular dynamics (MD) simulations assessed the stability of DAH7PS-ligand complexes. The complexes were further evaluated in terms of their binding affinity, Lipinski's Rule of Five, and ADMET properties.

Results: A total of 54 novel drug targets with desirable properties were identified. DAH7PS was selected for further investigation, and virtual screening of StreptomeDB compounds yielded 36 high-affinity binding of the ligands. Two small molecules, 6,8-Dihydroxyisocoumarin-3-carboxylic acid and Epicatechin, also showed favorable RO5 and ADMET properties. MD simulations confirmed the stability and reliability of DAH7PS-ligand complexes, indicating their potential as inhibitors.

Conclusion: This study identified 54 novel drug targets against H. pylori. The DAH7PS protein as a promising drug target was evaluated using a computer-aided drug design. 6,8-Dihydroxyisocoumarin-3-carboxylic acid and Epicatechin demonstrated desirable properties and stable interactions, highlighting their potential to inhibit DAH7PS as an essential protein. Undoubtedly, more experimental validations are needed to advance these findings into practical therapies for treating drug-resistant H. pylori.

背景:幽门螺杆菌是一种与严重胃肠道疾病和恶性肿瘤相关的细菌,由于其抗生素耐药率不断上升,给研究带来了巨大挑战。本研究旨在利用基于结构的虚拟筛选(SBVS)方法确定幽门螺杆菌的潜在药物靶点和抑制剂:方法:利用 EDGAR 数据库对 132 个幽门螺杆菌基因组进行了核心蛋白组分析。方法:利用 EDGAR 数据库对 132 个幽门螺杆菌基因组进行了核心蛋白质组分析,确定了基本基因,并排除了人类和肠道微生物同源蛋白。基于结构的虚拟筛选(SBVS)方法选择了参与莽草酸途径的 DAH7PS 蛋白。通过同源建模(基于 PDB ID:5UXM)预测了该蛋白质的三级结构。使用 AutoDock Vina 工具进行分子对接,在 StreptomeDB 化合物中找出 DAH7PS 的潜在抑制剂。分子动力学(MD)模拟评估了 DAH7PS 配体复合物的稳定性。这些复合物的结合亲和力、利平斯基五法则和 ADMET 特性得到了进一步评估:结果:共鉴定出 54 个具有理想特性的新型药物靶点。结果:共鉴定出 54 个具有理想特性的新型药物靶点,并选择 DAH7PS 作为进一步研究的对象。6,8-二羟基异香豆素-3-羧酸和表儿茶素这两种小分子也显示出良好的 RO5 和 ADMET 特性。MD 模拟证实了 DAH7PS 配体复合物的稳定性和可靠性,表明它们具有作为抑制剂的潜力:本研究发现了 54 个新的幽门螺杆菌药物靶点。结论:本研究发现了 54 种新的幽门螺杆菌药物靶点,并使用计算机辅助药物设计对 DAH7PS 蛋白作为一种有前景的药物靶点进行了评估。6,8-二羟基异香豆素-3-羧酸和表儿茶素表现出了理想的特性和稳定的相互作用,突出了它们抑制作为重要蛋白质的 DAH7PS 的潜力。毫无疑问,要将这些发现转化为治疗耐药性幽门螺杆菌的实用疗法,还需要更多的实验验证。
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引用次数: 0
Editorial: Women in bioinformatics. 社论:生物信息学领域的女性。
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-10-08 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1499514
Irma Martínez-Flores, Constanza Cárdenas Carvajal, Viviana Monje-Galvan
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引用次数: 0
In silico PCR analysis: a comprehensive bioinformatics tool for enhancing nucleic acid amplification assays. In silico PCR analysis: a comprehensive bioinformatics tool for enhancing nucleiss acid amplification assays.
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-10-07 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1464197
Ruslan Kalendar, Alexandr Shevtsov, Zhenis Otarbay, Aisulu Ismailova

Nucleic acid amplification assays represent a pivotal category of methodologies for targeted sequence detection within contemporary biological research, boasting diverse utility in diagnostics, identification, and DNA sequencing. The foundational principles of these assays have been extrapolated to various simple and intricate nucleic acid amplification technologies. Concurrently, a burgeoning trend toward computational or virtual methodologies is exemplified by in silico PCR analysis. In silico PCR analysis is a valuable and productive adjunctive approach for ensuring primer or probe specificity across a broad spectrum of PCR applications encompassing gene discovery through homology analysis, molecular diagnostics, DNA profiling, and repeat sequence identification. The prediction of primer and probe sensitivity and specificity necessitates thorough database searches, accounting for an optimal balance of mismatch tolerance, sequence similarity, and thermal stability. This software facilitates in silico PCR analyses of both linear and circular DNA templates, including bisulfited treatment DNA, enabling multiple primer or probe searches within databases of varying scales alongside advanced search functionalities. This tool is suitable for processing batch files and is essential for automation when working with large amounts of data.

核酸扩增检测是当代生物研究中一类重要的定向序列检测方法,在诊断、鉴定和 DNA 测序方面具有多种用途。这些检测方法的基本原理已被推广到各种简单和复杂的核酸扩增技术中。与此同时,计算或虚拟方法的趋势也在蓬勃发展,硅 PCR 分析就是一个例子。在广泛的 PCR 应用中,包括通过同源性分析发现基因、分子诊断、DNA 分析和重复序列鉴定,硅 PCR 分析是确保引物或探针特异性的一种有价值、有成效的辅助方法。要预测引物和探针的灵敏度和特异性,就必须进行全面的数据库搜索,在错配容限、序列相似性和热稳定性之间取得最佳平衡。该软件有助于对线性和环状 DNA 模板(包括双硫化处理 DNA)进行硅 PCR 分析,可在不同规模的数据库中进行多种引物或探针搜索,并具有高级搜索功能。该工具适用于处理批处理文件,是处理大量数据时实现自动化的必备工具。
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引用次数: 0
Discovery of plasma biomarkers related to blood-brain barrier dysregulation in Alzheimer's disease. 发现与阿尔茨海默病血脑屏障失调有关的血浆生物标志物。
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-10-04 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1463001
Yuet Ruh Dan, Keng-Hwee Chiam

Introduction: Blood-based biomarkers are quantitative, non-invasive diagnostic tools. This study aimed to identify candidate biomarkers for Alzheimer's disease (AD) using publicly available omics datasets, using the hypothesis that with blood-brain barrier dysfunction in AD, brain-synthesized proteins can leak into plasma for detection.

Methods: Differential abundance results of plasma and brain proteomic datasets were integrated to obtain a list of potential biomarkers. Biological validity was investigated with intercellular communication and gene regulatory analyses on brain single-cell transcriptomics data.

Results: Five proteins (APOD, B2M, CFH, CLU, and C3) fit biomarker criteria. 4 corresponding transcripts (APOD, B2M, CLU, and C3) were overexpressed in AD astrocytes, mediated by AD-related dysregulations in transcription factors regulating neuroinflammation. Additionally, CLU specifically induced downstream expression of neuronal death genes.

Discussion: In conclusion, a 5-protein panel is shown to effectively identify AD patients, with evidence of disease specificity and biological validity. Future research should investigate the mechanism of protein leakage through the blood-brain barrier.

简介基于血液的生物标记物是一种定量、非侵入性的诊断工具。本研究的目的是利用公开的全息数据集确定阿尔茨海默病(AD)的候选生物标志物,其假设是随着AD患者血脑屏障功能障碍,大脑合成的蛋白质会渗入血浆以供检测:方法:整合血浆和大脑蛋白质组数据集的丰度差异结果,得出潜在生物标记物列表。通过对脑单细胞转录组学数据进行细胞间通讯和基因调控分析,研究其生物学有效性:结果:5种蛋白质(APOD、B2M、CFH、CLU和C3)符合生物标记物标准。4种相应的转录本(APOD、B2M、CLU和C3)在AD星形胶质细胞中过度表达,这是由与AD相关的调节神经炎症的转录因子失调介导的。此外,CLU还能特异性诱导神经元死亡基因的下游表达:总之,5种蛋白面板可有效识别AD患者,并证明了疾病特异性和生物学有效性。未来的研究应探讨蛋白质通过血脑屏障渗漏的机制。
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引用次数: 0
A time-calibrated phylogeny of the diversification of Holoadeninae frogs. 蛙类 Holoadeninae 多样化的时间校准系统发育。
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-10-02 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1441373
Júlio C M Chaves, Fábio Hepp, Carlos G Schrago, Beatriz Mello

The phylogeny of the major lineages of Amphibia has received significant attention in recent years, although evolutionary relationships within families remain largely neglected. One such overlooked group is the subfamily Holoadeninae, comprising 73 species across nine genera and characterized by a disjunct geographical distribution. The lack of a fossil record for this subfamily hampers the formulation of a comprehensive evolutionary hypothesis for their diversification. Aiming to fill this gap, we inferred the phylogenetic relationships and divergence times for Holoadeninae using molecular data and calibration information derived from the fossil record of Neobatrachia. Our inferred phylogeny confirmed most genus-level associations, and molecular dating analysis placed the origin of Holoadeninae in the Eocene, with subsequent splits also occurring during this period. The climatic and geological events that occurred during the Oligocene-Miocene transition were crucial to the dynamic biogeographical history of the subfamily. However, the wide highest posterior density intervals in our divergence time estimates are primarily attributed to the absence of Holoadeninae fossil information and, secondarily, to the limited number of sampled nucleotide sites.

近年来,两栖动物主要品系的系统发育受到了极大关注,但科内的进化关系在很大程度上仍被忽视。Holoadeninae 亚科就是这样一个被忽视的亚科,该亚科由 9 个属 73 个种组成,地理分布不均。该亚科化石记录的缺乏阻碍了对其多样化提出一个全面的进化假说。为了填补这一空白,我们利用分子数据和来自新蝙蝠科化石记录的校准信息,推断了新蝙蝠科(Holoadeninae)的系统发生关系和分化时间。我们推断的系统发育证实了大多数属一级的联系,分子年代分析将 Holoadeninae 的起源定为始新世,随后的分裂也发生在这一时期。发生在渐新世-中新世过渡时期的气候和地质事件对该亚科的动态生物地理历史至关重要。然而,我们对分化时间估计的最高后验密度区间较宽,这主要是由于缺乏 Holoadeninae 的化石信息,其次是由于采样的核苷酸位点数量有限。
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引用次数: 0
SciJava Ops: an improved algorithms framework for Fiji and beyond. SciJava Ops:斐济及其他地区的改进算法框架。
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-09-27 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1435733
Gabriel J Selzer, Curtis T Rueden, Mark C Hiner, Edward L Evans, David Kolb, Marcel Wiedenmann, Christian Birkhold, Tim-Oliver Buchholz, Stefan Helfrich, Brian Northan, Alison Walter, Johannes Schindelin, Tobias Pietzsch, Stephan Saalfeld, Michael R Berthold, Kevin W Eliceiri

Decades of iteration on scientific imaging hardware and software has yielded an explosion in not only the size, complexity, and heterogeneity of image datasets but also in the tooling used to analyze this data. This wealth of image analysis tools, spanning different programming languages, frameworks, and data structures, is itself a problem for data analysts who must adapt to new technologies and integrate established routines to solve increasingly complex problems. While many "bridge" layers exist to unify pairs of popular tools, there exists a need for a general solution to unify new and existing toolkits. The SciJava Ops library presented here addresses this need through two novel principles. Algorithm implementations are declared as plugins called Ops, providing a uniform interface regardless of the toolkit they came from. Users express their needs declaratively to the Op environment, which can then find and adapt available Ops on demand. By using these principles instead of direct function calls, users can write streamlined workflows while avoiding the translation boilerplate of bridge layers. Developers can easily extend SciJava Ops to introduce new libraries and more efficient, specialized algorithm implementations, even immediately benefitting existing workflows. We provide several use cases showing both user and developer benefits, as well as benchmarking data to quantify the negligible impact on overall analysis performance. We have initially deployed SciJava Ops on the Fiji platform, however it would be suitable for integration with additional analysis platforms in the future.

数十年来,科学成像硬件和软件的迭代不仅带来了图像数据集的规模、复杂性和异质性的激增,也带来了用于分析这些数据的工具的激增。丰富的图像分析工具涵盖了不同的编程语言、框架和数据结构,对于数据分析师来说,这本身就是一个问题,他们必须适应新技术并整合已有的例程,以解决日益复杂的问题。虽然有许多 "桥接 "层可以统一流行的工具对,但仍需要一个通用的解决方案来统一新的和现有的工具包。本文介绍的 SciJava Ops 库通过两个新颖的原则满足了这一需求。算法实现被声明为名为 Ops 的插件,无论它们来自哪个工具包,都能提供统一的接口。用户以声明的方式向 Op 环境表达他们的需求,Op 环境就能根据需求找到并调整可用的 Ops。通过使用这些原则而不是直接调用函数,用户可以编写精简的工作流程,同时避免桥接层的翻译模板。开发人员可以轻松扩展 SciJava Ops,以引入新的库和更高效、更专业的算法实现,甚至立即使现有的工作流程受益。我们提供了几个使用案例,展示了用户和开发人员的收益,并提供了基准数据,量化了对整体分析性能的微不足道的影响。我们最初在斐济平台上部署了 SciJava Ops,但它也适合在未来与其他分析平台集成。
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引用次数: 0
Pangenome comparison via ED strings. 通过 ED 字符串进行泛基因组比较。
IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2024-09-26 eCollection Date: 2024-01-01 DOI: 10.3389/fbinf.2024.1397036
Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P Pissis, Jakub Radoszewski, Michelle Sweering, Wiktor Zuba

Introduction: An elastic-degenerate (ED) string is a sequence of sets of strings. It can also be seen as a directed acyclic graph whose edges are labeled by strings. The notion of ED strings was introduced as a simple alternative to variation and sequence graphs for representing a pangenome, that is, a collection of genomic sequences to be analyzed jointly or to be used as a reference.

Methods: In this study, we define notions of matching statistics of two ED strings as similarity measures between pangenomes and, consequently infer a corresponding distance measure. We then show that both measures can be computed efficiently, in both theory and practice, by employing the intersection graph of two ED strings.

Results: We also implemented our methods as a software tool for pangenome comparison and evaluated their efficiency and effectiveness using both synthetic and real datasets.

Discussion: As for efficiency, we compare the runtime of the intersection graph method against the classic product automaton construction showing that the intersection graph is faster by up to one order of magnitude. For showing effectiveness, we used real SARS-CoV-2 datasets and our matching statistics similarity measure to reproduce a well-established clade classification of SARS-CoV-2, thus demonstrating that the classification obtained by our method is in accordance with the existing one.

引言弹性退化(ED)字符串是一组字符串的序列。它也可以看作是一个有向无环图,其边缘用字符串标记。ED 字符串的概念是作为变异图和序列图的一种简单替代方法而提出的,用于表示庞基因组,即需要联合分析或用作参考的基因组序列集合:在这项研究中,我们定义了两个 ED 字符串的匹配统计量概念,将其作为庞基因组之间的相似性度量,并由此推断出相应的距离度量。然后,我们证明了通过使用两个 ED 字符串的交集图,可以在理论和实践中高效计算这两个度量:结果:我们还将我们的方法作为一种软件工具进行了庞基因组比较,并使用合成数据集和真实数据集评估了这些方法的效率和有效性:在效率方面,我们将交集图方法的运行时间与经典的乘积自动机构造进行了比较,结果显示交集图的速度快达一个数量级。在有效性方面,我们使用真实的 SARS-CoV-2 数据集和我们的匹配统计相似性度量重现了 SARS-CoV-2 的一个成熟的支系分类,从而证明我们的方法所获得的分类与现有的分类是一致的。
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引用次数: 0
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