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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Videos

basicsynbio and the BASIC SEVA collection: software and vectors for an established DNA assembly method.

Matthew C Haines1,2, Benedict Carling3, James Marshall3

  • 1Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, London SW7 2AZ, UK.

Synthetic Biology (Oxford, England)
|November 16, 2022
PubMed
Summary

basicsynbio software facilitates standardized deoxyribonucleic acid (DNA) assembly using the Biopart Assembly Standard for Idempotent Cloning (BASIC) method. This open-source tool simplifies the design and automation of complex biological constructs for bioengineering applications.

Keywords:
DNA assemblybioinformaticscloningsynthetic biologyvectors

Related Experiment Videos

Area of Science:

  • Synthetic Biology
  • Molecular Biology
  • Bioengineering

Background:

  • Standardized DNA assembly methods are crucial for efficient synthetic biology workflows.
  • The Biopart Assembly Standard for Idempotent Cloning (BASIC) offers a modular, accurate, and automatable approach to DNA assembly.
  • Existing tools may lack comprehensive features for designing and implementing BASIC constructs.

Purpose of the Study:

  • To introduce basicsynbio, an open-source software for designing DNA constructs using the BASIC assembly standard.
  • To provide a user-friendly platform for both programmatic and graphical design of BASIC assemblies.
  • To facilitate the creation and automation of synthetic biology experiments.

Main Methods:

  • Development of basicsynbio, including a Web App and Python Package.
  • Implementation of drag-and-drop functionality and programmatic design options.
  • Integration of exception handling for common design errors and generation of liquid-handling instructions based on the BasicBuild Open Standard.
  • Demonstration using the Standard European Vector Architecture (SEVA) collection.

Main Results:

  • basicsynbio enables easy design and assembly of BASIC DNA constructs.
  • The software supports programmatic access to parts and linkers, including custom designs.
  • Generated instructions are compatible with automated liquid-handling platforms.
  • A collection of 30 BASIC SEVA vectors was assembled and made available via Addgene.

Conclusions:

  • basicsynbio provides a powerful and accessible environment for designing DNA assemblies.
  • The software streamlines the Design-Build-Test-Learn cycle in synthetic biology.
  • It supports diverse bioengineering applications through standardized and modular DNA assembly.