对弦集的BWT变体的调查
Davide Cenzato1, Zsuzsanna Lipták2
1Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University, Venice, Italy.
Bioinformatics (Oxford, England)
|May 24, 2024
概括
对BWT变体的生物信息学工具产生非等效的结果,影响序列收集分析. 在BWT变体中的差异显著影响运行次数,在数据集中变化的幅度高达4.2倍.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 字符串处理 字符串处理
背景情况:
- 生物信息学研究越来越多地侧重于序列集合,而不是单个序列.
- 洞穴轮转换 (BWT) 对字符串处理至关重要,许多工具都是为序列集合开发的.
- 现有的BWT工具经常计算非等效的变体,导致输出和参数的显著差异,例如运行次数.
研究的目的:
- 为了研究和比较不同的BWT变体,用于用于弦集合的生物信息学工具.
- 突出BWT变体之间的差异及其对关键参数的影响.
- 评估输入数据顺序对BWT计算的影响.
主要方法:
- 研究了18个专门的工具来计算字符串集合的BWT.
- 识别和分类了6种不同的BWT变体.
- 在8个现实生物数据集上进行了BWT变体的理论和实践比较.
- 在不同的BWT变体中分析了运行次数 (r) 的变化.
主要成果:
- 在18个研究的工具中确定了6种不同的BWT变体.
- 证明了BWT变体之间的显著差异,特别是在许多类似短序的集合上.
- 观察到运行次数 (r) 的实质性变化,乘法因子高达4.2.
- 发现一些BWT变体对序列收集的输入顺序敏感.
结论:
- 选择BWT变体对序列收集的分析产生重大影响.
- 机械水务工具之间的差异可能导致无法比较的结果,并影响下游分析.
- 标准化或明确的BWT变体的文档对于可复制生物信息学研究至关重要.
相关概念视频
Types of Surveys
45
Surveys are essential for marking property boundaries near water bodies. Different types of surveys are defined, each with its own function. Land surveys mark the property boundaries, while route surveys determine the position of properties on nearby highways. Topographic surveys create maps by capturing the three-dimensional features of the land. Hydrographic surveys focus on the shapes of underwater areas and the movement of streams through the properties. Mine surveys determine the relative...
45
Data Collection by Survey
6.4K
The systematic method of obtaining and analyzing accurate information of a population is called data collection. A survey is a standard method of data collection that involves collecting information from a target human population about their experience, opinion, or knowledge of a product, service, or process. The responses are recorded and interpreted. The most common survey examples are written questionnaires, face-to-face or telephonic conversations, focus groups, and electronic (e-mail or...
6.4K
Wald-Wolfowitz Runs Test I
641
The Wald-Wolfowitz test, also known as the runs test, is a nonparametric statistical test used to assess the randomness of a sequence of two different types of elements (e.g., positive/negative values, successes/failures). It examines whether the order of the elements in a sequence is random or if there is a pattern or trend present. This nonparametric test applies to any ordered data despite the population and sample data distribution, even if a higher sample size is available.
The test works...
The test works...
641
Wald-Wolfowitz Runs Test II
227
The Wald-Wolfowitz runs test, commonly referred to as the runs test, is a nonparametric test used to assess the randomness of ordered data. The test evaluates the number of runs, which are consecutive sequences of similar elements within the data. If the number of runs is significantly higher or lower than expected, the data is considered non-random, indicating a detectable pattern or structure.
For binary data, runs are identified using symbols such as + and −, or equivalently, 1s and...
For binary data, runs are identified using symbols such as + and −, or equivalently, 1s and...
227
Data Collection by Observations
11.9K
Data collection refers to a systematic way of obtaining, observing, measuring, and analyzing accurate information. Observational studies are one of the most widely used methods of data collection. It involves collecting data by observing the behavior and physical characteristics of a sample without making any modifications to the sample.
An astronomer viewing the motion and brightness of stars in the sky and recording the data is an example of observational data collection. A botanist recording...
An astronomer viewing the motion and brightness of stars in the sky and recording the data is an example of observational data collection. A botanist recording...
11.9K
Genome-wide Association Studies-GWAS
13.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
13.3K


