Related Experiment Video
Updated: Jun 10, 2026
10:10
HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
Published on: March 31, 2019
Targeted identification of genomic regions using TAGdb
Daniel J Marshall1, Alice Hayward, Dominic Eales
1University of Queensland, Australian Centre for Plant Functional Genomics, School of Land, Crop and Food Sciences, Brisbane, QLD 4067, Australia. dave.edwards@uq.edu.au.
Plant Methods
|August 24, 2010
Summary
Researchers can now identify genes and promoters cost-effectively using second-generation sequencing (SGS) paired-read genome tags. This method bypasses the need for whole genome assembly, especially for complex plant genomes.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Second-generation sequencing (SGS) facilitates cost-effective genome sequencing and gene identification.
- Whole genome assembly remains expensive, particularly for complex plant genomes.
Purpose of the Study:
- To develop a cost-effective method for identifying genes and promoters in large, complex plant genomes.
- To provide a tool for researchers to identify specific DNA sequences without full genome assembly.
Main Methods:
- Development of an online database, TAGdb.
- Utilizing paired-read sequences from SGS to identify shared identity with query sequences.
- Generating genome tags for primer design.
Main Results:
- TAGdb enables the identification of paired-read sequences matching a query.
- Identified tags can be used to design primers for PCR amplification.
- This approach facilitates gene and promoter discovery.
Conclusions:
- Large-scale paired-read genome tags from SGS offer a cost-effective approach.
- This method is suitable for identifying genes and promoters in complex or orphan species.
- Eliminates the requirement for whole genome assembly.
