Semashko Tatiana A, Fisunov Gleb Y, Shevelev Georgiy Y, Govorun Vadim M
Research Institute for Systems Biology and Medicine, Moscow, Russian Federation.
Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation.
BMC Bioinformatics. 2025 Jan 23;26(1):27. doi: 10.1186/s12859-025-06049-9.
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.
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.
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 .
目前，合成基因组学是一个快速发展的领域。其主要任务，如合成序列的设计以及从合成寡核苷酸组装DNA序列，都需要专门的软件。在本文中，我们展示了一个带有图形界面的程序，它能让非生物信息学专业人员执行合成基因组学所需的任务。
我们开发了BAC-browser v.2.1。它有助于设计核苷酸序列，并具备以下工具：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，以及可视化限制酶切位点、GC组成、GC偏移和二级结构。为了组装DNA序列，创建了一个片段化工具：将其常规分解为特定长度的寡核苷酸，并分解为具有热力学比对的寡核苷酸。我们展示了在BAC-browser的不同模式下设计DNA片段组装的可能性。
BAC-browser拥有大量用于系统基因组学领域工作的工具，可通过直接链接https://sysbiomed.ru/upload/BAC-browser-2.1.zip免费获取。
