BAC-browser: the tool for synthetic biology.

IF 3.3 3区生物学 Q2 BIOCHEMICAL RESEARCH METHODS BMC Bioinformatics Pub Date : 2025-01-23 DOI:10.1186/s12859-025-06049-9

Tatiana A Semashko, Gleb Y Fisunov, Georgiy Y Shevelev, Vadim M Govorun

{"title":"BAC-browser: the tool for synthetic biology.","authors":"Tatiana A Semashko, Gleb Y Fisunov, Georgiy Y Shevelev, Vadim M Govorun","doi":"10.1186/s12859-025-06049-9","DOIUrl":null,"url":null,"abstract":"Background: Currently, synthetic genomics is a rapidly developing field. Its main tasks, such as the design of synthetic sequences and the assembly of DNA sequences from synthetic oligonucleotides, require specialized software. In this article, we present a program with a graphical interface that allows non-bioinformatics to perform the tasks needed in synthetic genomics.Results: We developed BAC-browser v.2.1. It helps to design nucleotide sequences and features the following tools: generate nucleotide sequence from amino acid sequences using a codon frequency table for a specific organism, as well as visualization of restriction sites, GC composition, GC skew and secondary structure. To assemble DNA sequences, a fragmentation tool was created: regular breakdown into oligonucleotides of a certain length and breakdown into oligonucleotides with thermodynamic alignment. We demonstrate the possibility of DNA fragments assemblies designed in different modes of BAC-browser.Conclusions: The BAC-browser has a large number of tools for working in the field of systemic genomics and is freely available at the link with a direct link https://sysbiomed.ru/upload/BAC-browser-2.1.zip .","PeriodicalId":8958,"journal":{"name":"BMC Bioinformatics","volume":"26 1","pages":"27"},"PeriodicalIF":3.3000,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758742/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12859-025-06049-9","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}

引用次数: 0

Abstract

Background: Currently, synthetic genomics is a rapidly developing field. Its main tasks, such as the design of synthetic sequences and the assembly of DNA sequences from synthetic oligonucleotides, require specialized software. In this article, we present a program with a graphical interface that allows non-bioinformatics to perform the tasks needed in synthetic genomics.

Results: We developed BAC-browser v.2.1. It helps to design nucleotide sequences and features the following tools: generate nucleotide sequence from amino acid sequences using a codon frequency table for a specific organism, as well as visualization of restriction sites, GC composition, GC skew and secondary structure. To assemble DNA sequences, a fragmentation tool was created: regular breakdown into oligonucleotides of a certain length and breakdown into oligonucleotides with thermodynamic alignment. We demonstrate the possibility of DNA fragments assemblies designed in different modes of BAC-browser.

Conclusions: The BAC-browser has a large number of tools for working in the field of systemic genomics and is freely available at the link with a direct link https://sysbiomed.ru/upload/BAC-browser-2.1.zip .

Abstract Image

查看原文

微信好友朋友圈 QQ好友复制链接

本刊更多论文

bac浏览器：合成生物学的工具。

背景：目前合成基因组学是一个快速发展的领域。它的主要任务，如设计合成序列和从合成寡核苷酸组装DNA序列，需要专门的软件。在这篇文章中，我们提出了一个具有图形界面的程序，允许非生物信息学执行合成基因组学所需的任务。结果：我们开发了BAC-browser v.2.1。它有助于设计核苷酸序列，并具有以下工具：使用特定生物体的密码子频率表从氨基酸序列生成核苷酸序列，以及限制位点、GC组成、GC倾斜和二级结构的可视化。为了组装DNA序列，我们创建了一种片段化工具：有规律地分解成一定长度的寡核苷酸，并分解成具有热力学比对的寡核苷酸。我们展示了在不同模式的bac -浏览器中设计DNA片段组装的可能性。结论：BAC-browser拥有大量用于系统基因组学领域工作的工具，并且可以通过直接链接https://sysbiomed.ru/upload/BAC-browser-2.1.zip免费获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文去求助

来源期刊

BMC Bioinformatics 生物-生化研究方法

CiteScore

5.70

自引率

3.30%

发文量

506

审稿时长

4.3 months

期刊介绍： BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.