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Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost

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BMC BIOINFORMATICS 2006年第1期7卷 524-524页

作者： Yamada, Shinsuke Gotoh, Osamu Yamana, Hayato Waseda Univ Grad Sch Sci & Engn Dept Comp Sci Shinjuku Ku Tokyo 1698555 Japan Natl Inst AIST CBRC Koto Ku Tokyo 1350064 Japan Kyoto Univ Grad Sch Informat Dept Intelligence Sci & Technol Sakyo Ku Kyoto 6068501 Japan

Background: Multiple sequence alignment (MSA) is a useful tool in bioinformatics. Although many MSA algorithms have been developed, there is still room for improvement in accuracy and speed. In the alignment of a family of protein sequences, global MSA algorithms perform better than local ones in many cases, while local ones perform better than global ones when some sequences have long insertions or deletions (indels) relative to others. Many recent leading MSA algorithms have incorporated pairwise alignment information obtained from a mixture of sources into their scoring system to improve accuracy of alignment containing long indels. Results: We propose a novel group-to-group sequence alignment algorithm that uses a piecewise linear gap cost. We developed a program called PRIME, which employs our proposed algorithm to optimize the well-defined sum-of-pairs score. PRIME stands for Profile-based Randomized Iteration MEthod. We evaluated PRIME and some recent MSA programs using BAliBASE version 3.0 and PREFAB version 4.0 benchmarks. The results of benchmark tests showed that PRIME can construct accurate alignments comparable to the most accurate programs currently available, including L-INS-i of MAFFT, ProbCons, and T-Coffee. Conclusion: PRIME enables users to construct accurate alignments without having to employ pairwise alignment information. PRIME is available at http://***/.

关键词： Reference alignment Multiple sequence alignment Program sequence alignment algorithm Dynamic Programming Matrix Column Score

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A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

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BMC BIOINFORMATICS 2002年第18期3卷 1-1页

作者： Eddy, SR Washington Univ Sch Med Howard Hughes Med Inst St Louis MO 63110 USA Washington Univ Sch Med Dept Genet St Louis MO 63110 USA

Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N-3) in memory. This is only practical for small RNAs. Results: I describe a divide and conquer variant of the alignment algorithm that is analogous to memory-efficient Myers/Miller dynamic programming algorithms for linear sequence alignment. The new algorithm has an O(N-2 log N) memory complexity, at the expense of a small constant factor in time. Conclusions: Optimal ribosomal RNA structural alignments that previously required up to 150 GB of memory now require less than 270 MB.

关键词： alignment algorithm Parse Tree Guide Tree Optimal alignment sequence alignment algorithm

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Facility Layout Based on sequence Analysis:Design of Flowshops

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Journal of Shanghai Jiaotong university(Science) 2009年第6期14卷 686-689页

作者：周瑾吴智铭 School of Electronic and Electrical Engineering Shanghai Second Polytechnic University Department of Automation Shanghai Jiaotong University

A computer-aided method to design a hybrid layout--tree-shape planar flowlines is presented. In newtype fiowshop layout, the common machines shared by several flowlines could be located together in functional sections. The approach combines traditional cell formation techniques with sequence alignment algorithms. Firstly, a sequence analysis based cell formation procedure is adopted; then the operation sequences for parts are aligned to maximize machines adjacency in hyperedge representations; finally a tree-shape planar flowline will be obtained for each part family. With the help of a sample of operation sequences obtained from industry, this algorithm is illustrated.

关键词： workshop layout flowlines sequence analysis sequence alignment algorithm

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ASTENS-BWA: Searching partial syntactic similar regions between source code fragments via AST-based encoded sequence alignment

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SCIENCE OF COMPUTER PROGRAMMING 2022年 222卷

作者： Yu, Yaoshen Huang, Zhiqiu Shen, Guohua Li, Weiwei Shao, Yichao Nanjing Univ Aeronaut & Astronaut Coll Comp Sci & Technol Nanjing Peoples R China Collaborat Innovat Ctr Novel Software Technol & In Nanjing Peoples R China Minist Ind & Informat Technol Key Lab Safety Crit Software Nanjing Peoples R China

Code search is a common activity in software development, and code-to-code search can benefit in a wide range of use-case scenarios. Code-to-code search uses a code fragment as the query for searching similar code fragments from large corpora. The results of a search can be applied to some software engineering tasks, such as search-based code recommendation, data-driven program repairing, and software plagiarism detection. To be put into daily use, the code-to-code search needs to find similar code fragments accurately and efficiently in a large dataset. Some search engines can locate exactly similar code, but are not able to search syntactical clones. Therefore, we propose ASTENS-BWA, a novel approach for searching syntactic similar code regions between code fragments via a tree-based sequence alignment. Source code has been transformed into a tree-based sequence that contains the structure information, and a sequence alignment algorithm has been applied to find similar regions. We evaluate ASTENS-BWA on three different tasks, the results demonstrate that our approach can find syntactical similar regions for programming code and retrieve similar code fragments fast and with high accuracy. As a code clone detection tool, ASTENS-BWA can report clone pairs in a high recall, but it needs manually check to reduce the false alarms. ASTENS-BWA is scalable and can report cloned code fragments in seconds for a code corpus of million lines of code. (C) 2022 Elsevier B.V. All rights reserved.

关键词： Code clone search Syntactical similarity Code representation model Abstract syntax tree sequence alignment algorithm

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A Deep Learning Framework With Visualisation for Uncovering Students' Learning Progression and Learning Bottlenecks

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JOURNAL OF EDUCATIONAL COMPUTING RESEARCH 2024年第1期62卷 223-249页

作者： Sit, Chun Yan Enoch Kong, Siu-Cheung Educ Univ Hong Kong Hong Kong Peoples R China Educ Univ Hong Kong Artificial Intelligence & Digital Competency Educ Dept Math & Informat Technol Tai Po 10 Lo Ping Rd Hong Kong Peoples R China

Educational process mining aims (EPM) to help teachers understand the overall learning process of their students. Although deep learning models have shown promising results in many domains, the event log dataset in many online courses may not be large enough for deep learning models to approximate the probability distribution of students' learning sequence due to a lack of participants. This study proposes a deep learning framework to help uncover the learning progression of learners. It aims to produce a graphical representation of the overall educational process from event logs. Our framework adopts the Smith-Waterman algorithm from the bioinformatics field to evaluate general learning sequences generated from deep learning models. Using our framework, we compare the performance of a deep learning model with the modified cross-attention layer and a model without modification and find that the modified model outperforms the other. The contribution of this framework is that it enables the use of neural architecture search techniques to uncover students' general learning sequence irrespective of the dataset's size. The framework also helps educators identify education materials that present as learning bottlenecks, enabling them to improve the materials and their respective layout order, thus facilitating student learning.

关键词： deep learning students' learning progression sequence alignment algorithm transformer learning bottlenecks educational process mining

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Privacy Oracle: a System for Finding Application Leaks with Black Box Differential Testing 08

Privacy Oracle: a System for Finding Application Leaks with ...

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15th ACM Conference on Computer and Communications Security

作者： Jung, Jaeyeon Sheth, Anmol Greenstein, Ben Wetherall, David Maganis, Gabriel Kohno, Tadayoshi Intel Res Seattle WA USA

ISBN: (纸本)9781595938107

We describe the design and implementation of Privacy Oracle, a system that reports oil application leaks of user information via the network traffic that they send. Privacy Oracle treats each application its a black box, without access to either its internal structure or Communication protocols. This means that it call be used over a broad range of applications and information leaks (i.e., not only Web traffic content or credit card numbers). To accomplish this, we develop it differential testing technique in which perturbations in the application inputs are mapped to perturbations in the application Outputs to discover likely leaks;we leverage alignment algorithms from computational biology to find high quality mappings between different byte-sequences efficiently. Privacy Oracle includes this technique and it virtual machine-based testing system. To evaluate it, we tested 26 popular applications, including system and file utilities, media players, and IM clients. We found that Privacy Oracle discovered many small and previously undisclosed information leaks. In several cases, these are leaks of directly identifying information that are regularly sent in the clear (without end-to-end encryption) and which Could make users vulnerable to tracking by third parties or providers.

关键词： Personal information leaks Black-box testing sequence alignment algorithm Differential fuzz testing Data loss prevention

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Parallelized pairwise sequence alignment using CUDA on multiple GPUs

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BMC BIOINFORMATICS 2009年第Sup7期10卷 1-1页

作者： Jung, Sungbo Univ Louisville Dept Comp Sci & Comp Engn Louisville KY 40292 USA

An abstract of a study related to parallelized pairwise sequence alignment by the use of compute unified device architecture (CUDA) on the multiple graphics processing units (GPUs), which was conducted by Sungbo Jung,... 详细信息

关键词： Graphic Processing Unit Pairwise sequence alignment Multiple GPUs sequence alignment algorithm Local sequence alignment

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PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

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BMC BIOINFORMATICS 2011年第1期12卷 1-6页

作者： Sipos, Botond Massingham, Tim Jordan, Gregory E. Goldman, Nick EMBL European Bioinformat Inst Hinxton England Biol Res Ctr Inst Genet Lab Mol Biodivers H-6701 Szeged Hungary

Background: The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fuels the need for more realistic and hence more complex simulations, adapted to particular situations, yet current software makes unreasonable assumptions such as homogeneous substitution dynamics or a uniform distribution of indels across the simulated sequences. This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity. Results: PhyloSim is an extensible framework for the Monte Carlo simulation of sequence evolution, written in R, using the Gillespie algorithm to integrate the actions of many concurrent processes such as substitutions, insertions and deletions. Uniquely among sequence simulation tools, PhyloSim can simulate arbitrarily complex patterns of rate variation and multiple indel processes, and allows for the incorporation of selective constraints on indel events. User-defined complex patterns of mutation and selection can be easily integrated into simulations, allowing PhyloSim to be adapted to specific needs. Conclusions: Close integration with R and the wide range of features implemented offer unmatched flexibility, making it possible to simulate sequence evolution under a wide range of realistic settings. We believe that PhyloSim will be useful to future studies involving simulated alignments.

关键词： Monte Carlo Simulation sequence Evolution Selective Constraint Gillespie algorithm sequence alignment algorithm

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Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements

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BMC BIOINFORMATICS 2007年第1期8卷 94-94页

作者： Doh, Sung Tae Zhang, Yunyu Temple, Matthew H. Cai, Li Rutgers State Univ Dept Biomed Engn Piscataway NJ 08854 USA Dana Farber Canc Inst Boston MA 02115 USA

Background: Completion of the human genome sequence along with other species allows for greater understanding of the biochemical mechanisms and processes that govern healthy as well as diseased states. The large size of the genome sequences has made them difficult to study using traditional methods. There are many studies focusing on the protein coding sequences, however, not much is known about the function of non-coding regions of the genome. It has been demonstrated that parts of the non-coding region play a critical role as gene regulatory elements. Enhancers that regulate transcription processes have been found in intergenic regions. Furthermore, it is observed that regulatory elements found in non-coding regions are highly conserved across different species. However, the analysis of these regulatory elements is not as straightforward as it may first seem. The development of a centralized resource that allows for the quick and easy retrieval of non-coding sequences from multiple species and is capable of handing multi-gene queries is critical for the analysis of non-coding sequences. Here we describe the development of a web-based non-coding sequence retrieval system. Results: This paper presents a Non-Coding sequences Retrieval System (NCSRS). The NCSRS is a web-based bioinformatics tool that performs fast and convenient retrieval of non-coding and coding sequences from multiple species related to a specific gene or set of genes. This tool has compiled resources from multiple sources into one easy to use and convenient web based interface. With no software installation necessary, the user needs only internet access to use this tool. Conclusion: The unique features of this tool will be very helpful for those studying gene regulatory elements that exist in non-coding regions. The web based application can be accessed on the internet at: http://***/ncsrs/.

关键词： Annotation Information sequence alignment algorithm Gene Regulatory Element Ensembl Annotation RefSeq Annotation

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生物DNA序列比对算法研究

生物DNA序列比对算法研究

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第二十一届中国数据库学术会议

作者：许龙飞段敏陈孝卫冉丽朱婵暨南大学计算机科学系

1引言DNA多序列比对是生物基因信息系统中,现代生物序列分析的重要内容,也是当今生物信息学研究的热点课题。通过多序列比对,可以预测新序列的结构和功能,可以分析序列之间的相似和同源关系,以及进行系统发育分析,多序列比对是一个具有... 详细信息

1引言DNA多序列比对是生物基因信息系统中,现代生物序列分析的重要内容,也是当今生物信息学研究的热点课题。通过多序列比对,可以预测新序列的结构和功能,可以分析序列之间的相似和同源关系,以及进行系统发育分析,多序列比对是一个具有高计算复杂度的组合优化问题。

关键词： Bioinformatics DNA sequence sequence alignment algorithm Data mining

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