{"title":"ReDtool:基于 Python 命令行的大型 DNA 序列限制性消化分析工具","authors":"Guntha Shiva Brahmam, Divya Mishra, Vikash Kumar Yadav","doi":"10.1007/s13562-024-00906-z","DOIUrl":null,"url":null,"abstract":"<p>Developing an in-silico restriction digestion tool is vital in modern molecular biology and genomics. We develop ReDtool, a Python 3-based command-line toolkit to simulate restriction digestion processes. ReDtool offers a virtual digestion function, simulating restriction digestion on a provided sequence by specifying any desired restriction site. We validated the output of ReDtool experimentally using restriction analysis and Sanger sequencing. ReDtool processes large genomic sequences efficiently, accepting FASTA or text format as input. The output file includes detailed information such as restriction site position, fragment length, and fragment sequence. With its high throughput and precision, ReDtool enables comprehensive restriction digestion analysis of chromosomes or genomes, addressing a critical need in genomic research with its straightforward approach (https://github.com/CBL205NIPGR/ReDtool).</p>","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":null,"pages":null},"PeriodicalIF":16.4000,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"ReDtool: a Python-based command line tool for restriction digestion analysis of large DNA sequences\",\"authors\":\"Guntha Shiva Brahmam, Divya Mishra, Vikash Kumar Yadav\",\"doi\":\"10.1007/s13562-024-00906-z\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>Developing an in-silico restriction digestion tool is vital in modern molecular biology and genomics. We develop ReDtool, a Python 3-based command-line toolkit to simulate restriction digestion processes. ReDtool offers a virtual digestion function, simulating restriction digestion on a provided sequence by specifying any desired restriction site. We validated the output of ReDtool experimentally using restriction analysis and Sanger sequencing. ReDtool processes large genomic sequences efficiently, accepting FASTA or text format as input. The output file includes detailed information such as restriction site position, fragment length, and fragment sequence. With its high throughput and precision, ReDtool enables comprehensive restriction digestion analysis of chromosomes or genomes, addressing a critical need in genomic research with its straightforward approach (https://github.com/CBL205NIPGR/ReDtool).</p>\",\"PeriodicalId\":1,\"journal\":{\"name\":\"Accounts of Chemical Research\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":16.4000,\"publicationDate\":\"2024-07-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Accounts of Chemical Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1007/s13562-024-00906-z\",\"RegionNum\":1,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Accounts of Chemical Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s13562-024-00906-z","RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
ReDtool: a Python-based command line tool for restriction digestion analysis of large DNA sequences
Developing an in-silico restriction digestion tool is vital in modern molecular biology and genomics. We develop ReDtool, a Python 3-based command-line toolkit to simulate restriction digestion processes. ReDtool offers a virtual digestion function, simulating restriction digestion on a provided sequence by specifying any desired restriction site. We validated the output of ReDtool experimentally using restriction analysis and Sanger sequencing. ReDtool processes large genomic sequences efficiently, accepting FASTA or text format as input. The output file includes detailed information such as restriction site position, fragment length, and fragment sequence. With its high throughput and precision, ReDtool enables comprehensive restriction digestion analysis of chromosomes or genomes, addressing a critical need in genomic research with its straightforward approach (https://github.com/CBL205NIPGR/ReDtool).
期刊介绍:
Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance.
Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.