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Background <p>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.</p> Results <p>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.</p> <p>We demonstrate the possibility of DNA fragments assemblies designed in different modes of BAC-browser.</p> Conclusions <p>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 <a href="https://sysbiomed.ru/upload/BAC-browser-2.1.zip">https://sysbiomed.ru/upload/BAC-browser-2.1.zip</a>.</p>

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BAC-browser: the tool for synthetic biology

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年1月23日

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

摘要

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.