BAC-browser: the tool for synthetic biology
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...
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| Format: | Article |
| Language: | English |
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BMC
2025-01-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06049-9 |
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| author | Tatiana A. Semashko Gleb Y. Fisunov Georgiy Y. Shevelev Vadim M. Govorun |
| author_facet | Tatiana A. Semashko Gleb Y. Fisunov Georgiy Y. Shevelev Vadim M. Govorun |
| author_sort | Tatiana A. Semashko |
| collection | DOAJ |
| description | 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 . |
| format | Article |
| id | doaj-art-1d3c8218bb744040a3f3237b1148fff1 |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-1d3c8218bb744040a3f3237b1148fff12025-01-26T12:54:53ZengBMCBMC Bioinformatics1471-21052025-01-0126111410.1186/s12859-025-06049-9BAC-browser: the tool for synthetic biologyTatiana A. Semashko0Gleb Y. Fisunov1Georgiy Y. Shevelev2Vadim M. Govorun3Research Institute for Systems Biology and MedicineResearch Institute for Systems Biology and MedicineInstitute of Chemical Biology and Fundamental MedicineResearch Institute for Systems Biology and MedicineAbstract 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 .https://doi.org/10.1186/s12859-025-06049-9Genome browserSequence editorLCR assemblyPCR assemblySynthetic biologySynthetic genomics |
| spellingShingle | Tatiana A. Semashko Gleb Y. Fisunov Georgiy Y. Shevelev Vadim M. Govorun BAC-browser: the tool for synthetic biology BMC Bioinformatics Genome browser Sequence editor LCR assembly PCR assembly Synthetic biology Synthetic genomics |
| title | BAC-browser: the tool for synthetic biology |
| title_full | BAC-browser: the tool for synthetic biology |
| title_fullStr | BAC-browser: the tool for synthetic biology |
| title_full_unstemmed | BAC-browser: the tool for synthetic biology |
| title_short | BAC-browser: the tool for synthetic biology |
| title_sort | bac browser the tool for synthetic biology |
| topic | Genome browser Sequence editor LCR assembly PCR assembly Synthetic biology Synthetic genomics |
| url | https://doi.org/10.1186/s12859-025-06049-9 |
| work_keys_str_mv | AT tatianaasemashko bacbrowserthetoolforsyntheticbiology AT glebyfisunov bacbrowserthetoolforsyntheticbiology AT georgiyyshevelev bacbrowserthetoolforsyntheticbiology AT vadimmgovorun bacbrowserthetoolforsyntheticbiology |