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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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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...
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Updated: Jan 8, 2026

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Protocol for extracting intergenic regions from annotated genomes using TIGRE.

Breno Dupin1, Matheus Sanita Lima2, Alexandre Rossi Paschoal3

  • 1Department of Computer Science, Federal University of Technology-Parana, Cornelio Procopio, Paraná 86300-000, Brazil.

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|December 20, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces TIGRE (Tool for Intergenic Region Extraction), a new protocol for extracting intergenic DNA sequences from genomes. The tool simplifies data preparation, sequence retrieval, and file merging for genomic analysis.

Keywords:
bioinformaticscomputer sciencesevolutionary biologygenomics

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Intergenic regions are crucial non-coding DNA sequences.
  • Efficient extraction of these regions is vital for genomic research.
  • Current methods may lack comprehensive functionality for intergenic region analysis.

Purpose of the Study:

  • To present a standardized protocol for extracting intergenic regions from annotated genomes.
  • To introduce the Tool for Intergenic Region Extraction (TIGRE) software.
  • To demonstrate TIGRE's utility in analyzing large-scale genomic datasets.

Main Methods:

  • Development and description of the TIGRE protocol for local installation and use.
  • Utilizing TIGRE commands: 'clean' for data preparation, 'extract' for sequence retrieval, 'getfasta' for nucleotide sequences, and 'combine' for GFF3 file merging.
  • Application of the protocol to 1,207 land plant mitochondrial genomes.

Main Results:

  • Successful implementation of a protocol for intergenic region extraction using TIGRE.
  • Demonstrated capability of TIGRE to process and extract sequences from a large collection of genomes.
  • Generated intergenic nucleotide sequences from land plant mitochondrial genomes.

Conclusions:

  • TIGRE provides a robust and efficient solution for intergenic region extraction.
  • The protocol facilitates downstream analyses of non-coding genomic elements.
  • This tool aids comparative genomics and evolutionary studies, particularly in plant mitochondria.