Creating De Novo Overlapped Genes

Logel, Dominic Y.; Jaschke, Paul R.

doi:10.1007/978-1-0716-2617-7_6

Cited by 2 publications

(2 citation statements)

References 38 publications

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“…Lastly, the VM is available to the students to use on their own machines if they want to pursue additional work after the course is completed. For the very same reasons, we have previously developed a VM for performing advanced machine learning work to enable research scientists to design overlapping genes 19 , 20 without the need for loading all the complex applications on their own computers, or the need to create a Linux partition if they do not already run this operating system.…”

Section: Practical Issues Of the Coursementioning

confidence: 99%

A bacterial genome assembly and annotation laboratory using a virtual machine

Trofimova

Kangachar

Weynberg

et al. 2023

Biochem Molecular Bio Educ

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With the global increase of infections caused by antibiotic‐resistant bacterial strains, there is an urgent need for new methods of tackling the issue. Genomic analysis of bacterial strains can help to understand their virulence and antibiotic resistance profile. Bioinformatic skills are in great demand across the biological sciences. We designed a workshop that allows university students to learn the process of genome assembly using command‐line tools within a virtual machine on a Linux operating system. We use Illumina and Nanopore short and long‐read raw sequences to reveal the advantages and disadvantages of short, long, and hybrid assembly methods. The workshop teaches how to assess read and assembly quality, perform genome annotation, and analyze pathogenicity, antibiotic and phage resistance. The workshop is intended for a five‐week teaching period and is concluded by a student poster presentation assessment.

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Section: Practical Issues Of the Coursementioning

confidence: 99%

A bacterial genome assembly and annotation laboratory using a virtual machine

Trofimova

Kangachar

Weynberg

et al. 2023

Biochem Molecular Bio Educ

Self Cite

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“…However, CAMEOS is a computationally intensive sequential code requiring several pre-computed inputs. More recently, an effort was made to distribute CAMEOS in a virtual machine to expand accessibility to the original software (Logel and Jaschke, 2023). Nevertheless, the original code remains limited in the ability to efficiently evaluate new gene pairs (Arbel-Groissman et al ., 2023).…”

Section: Introductionmentioning

confidence: 99%

GENTANGLE: integrated computational design of gene entanglements

Martí,

Hsu,

Rochereau

et al. 2023

Preprint

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SummaryThe design of two overlapping genes in a microbial genome is an emerging technique for adding more reliable control mechanisms in engineered organisms for increased safety. The design of functional gene pairs is a challenging procedure and computational design tools are used to improve the efficiency to deploy successful designs in genetically engineered systems. GENTANGLE (Gene Tuples ArraNGed in overLapping Elements) is a high performance containerized pipeline for the computational design of two overlapping genes translated in different reading frames of the genome. This new software package can be used to design and test gene entanglements for microbial engineering projects using arbitrary sets of user specified gene pairs.Availability and ImplementationThe GENTANGLE source code and its submodules are freely available on GitHub athttps://github.com/BiosecSFA/gentangle. The DATANGLE (DATA for genTANGLE) repository contains related data and results, and is freely available on GitHub athttps://github.com/BiosecSFA/datangle. The GENTANGLE repository wiki contains detailed instructions on how to use the container and the different components of software and data, including reproducing the results. The code is licensed under the GNU Affero General Public License version 3 (https://www.gnu.org/licenses/agpl.html).Contactmartimartine1@llnl.govandallen99@llnl.gov

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Creating De Novo Overlapped Genes

Cited by 2 publications

References 38 publications

A bacterial genome assembly and annotation laboratory using a virtual machine

A bacterial genome assembly and annotation laboratory using a virtual machine

GENTANGLE: integrated computational design of gene entanglements

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