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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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.
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
RNA-seq03:21

RNA-seq

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Related Experiment Video

Updated: May 30, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Filtering "genic" open reading frames from genomic DNA samples for advanced annotation.

Sara D'Angelo1, Nileena Velappan, Flavio Mignone

  • 1Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.

BMC Genomics
|August 4, 2011
PubMed
Summary
This summary is machine-generated.

This study presents a novel method using beta-lactamase to filter DNA for functional gene fragments, creating diverse open reading frame libraries for improved genome annotation and protein studies.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Protein Engineering

Background:

  • Accurate experimental gene annotation requires DNA encoding open reading frames (ORFs) in the correct frame.
  • Challenges include incorrect gene assignments and protein misfolding in heterologous hosts.
  • Expressing protein domains instead of full-length proteins can overcome misfolding issues.

Purpose of the Study:

  • To develop a method for isolating DNA encoding functional protein domains from complex DNA samples.
  • To create diverse genic open reading frame (ORF) libraries using a selectable folding reporter system.
  • To enhance the accessibility of the
  • Main_Methods

Main Methods:

  • Utilized randomly fragmented genomic DNA and beta-lactamase as a selectable folding reporter.
  • Cloned DNA fragments between leader sequences and the mature beta-lactamase gene.
  • Selected colonies for ampicillin resistance, indicating correct beta-lactamase folding and genic ORFs.

Main Results:

  • Demonstrated that beta-lactamase effectively filters for genic ORFs based on correct folding.
  • Showed that different leader sequences (Sec, TAT, SRP) enrich specific genic fragment subsets.
  • Confirmed that the majority of surviving colonies contained genic ORFs.

Conclusions:

  • The developed ORF library preparation method facilitates the identification and structural determination of functional genic ORFs.
  • Combined with screening methods, these libraries aid in high-throughput functional annotation of newly sequenced genomes.
  • This approach advances the study of the
  • Meta_Description