Similarity Detection in Biological Sequences using Parameterized Matching and Q-gram

机译：使用参数化匹配和Q-gram的生物序列相似性检测

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Whenever characterization of a new DNA sequence takes place then, database search is carried out to find whether homolog’s of gene is present or not. Various evolutions in this field have marked the shift from exact matching to a completely different concept, parameterized matching. Parameterized matching is detected by consistent renaming of text and pattern using bijective mapping. While finding matches between pattern and text, the PBMH-Hash algorithm results in frequent occurrence of false matches with large number of character comparison. This paper presents a new algorithm to detect similarity in biological sequences. The proposed algorithm is based on the concept of Berry-Ravindran algorithm and q-Gram. Analysis shows that our algorithm outperforms existing PBMH-Hash algorithm.

机译：每当对新的DNA序列进行表征时，就会进行数据库搜索以查找是否存在基因的同源物。该领域的各种发展标志着从精确匹配到完全不同的概念（参数化匹配）的转变。通过使用双射映射一致地重命名文本和模式，可以检测到参数化的匹配。在查找图案和文本之间的匹配项时，PBMH-Hash算法会导致错误匹配项频繁出现，并且会进行大量字符比较。本文提出了一种检测生物序列相似性的新算法。该算法基于Berry-Ravindran算法和q-Gram的概念。分析表明，我们的算法优于现有的PBMH-Hash算法。

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来源
《2018 Recent Advances on Engineering, Technology and Computational Sciences》|2018年|1-6|共6页
会议地点 Allahabad(IN)
作者
Rama Singh; Deepak Rai; Rajesh Prasad; Rajeev Singh;
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作者单位

Department of CSE, Ajay Kumar Garg Engineering College, Ghaziabad, India;

Department of CSE, Ajay Kumar Garg Engineering College, Ghaziabad, India;

School of IT Computing, American University of Nigeria, Yola, Nigeria;

Department of CSE, Ajay Kumar Garg Engineering College, Ghaziabad, India;

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原文格式 PDF
正文语种 eng
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关键词
Pattern matching; Microsoft Windows; Indexes; Time complexity; DNA; Biological information theory;

机译：模式匹配; Microsoft Windows;索引;时间复杂度; DNA;生物信息论;;

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专利

1. Bilateral similarity function: a novel and universal method for similarity analysis of biological sequences. [J] . Wang S, Tian F, Qiu Y, Journal of Theoretical Biology . 2010,第2期

机译：双边相似性函数：一种新颖且通用的生物序列相似性分析方法。
2. Frequency-based similarity for parameterized sequences: Formal framework, algorithms, and applications [J] . Greco G., Terracina G. Information Sciences: An International Journal . 2013,第Null期

机译：参数化序列的基于频率的相似性：正式框架，算法和应用
3. Structural parameterization and functional prediction of antigenic polypeptome sequences with biological activity through quantitative sequence-activity models (QSAM) by molecular electronegativity edge-distance vector (VMED) [J] . LI ZhiLiang, WU ShiRong, CHEN ZeCong, Science in China . 2007,第5期

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4. Similarity Detection in Biological Sequences using Parameterized Matching and Q-gram [C] . Rama Singh, Deepak Rai, Rajesh Prasad, Conference on Recent Advances on Engineering, Technology and Computational Sciences . 2018

机译：使用参数化匹配和Q-GRAM的生物序列中的相似性检测
5. High Performance and Scalable Matching and Assembly of Biological Sequences. [D] . Abu Doleh, Anas. 2016

机译：高性能，可扩展的生物序列匹配和组装。
6. Structural parameterization and functional prediction of antigenic polypeptome sequences with biological activity through quantitative sequence-activity models (QSAM) by molecular electronegativity edge-distance vector (VMED) [O] . ZhiLiang Li, ShiRong Wu, ZeCong Chen, -1

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7. Fast parameterized matching with q-grams [O] . Salmela Leena, Tarhio Jorma 2008

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8. Equipping Reserve Early Consequence Management Response Forces with State-Of-The-Art/Off-The-Shelf Nuclear, Biological and Chemical (NBC) Detection Equipment [R] . Ladd, C. B. 2001

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Similarity Detection in Biological Sequences using Parameterized Matching and Q-gram

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