Related Experiment Video
Updated: Jun 22, 2026
10:40
Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Published on: December 22, 2017
Reordering contigs of draft genomes using the Mauve aligner
Anna I Rissman1, Bob Mau, Bryan S Biehl
1Genome Evolution Laboratory, University of Wisconsin-Madison, 425G Henry Mall Suite 4400V, Madison, WI 53706, USA. rissman@wisc.edu
Bioinformatics (Oxford, England)
|June 12, 2009
Summary
Mauve Contig Mover offers a new automated method to arrange genome contigs using reference genomes. This tool aids in exploring draft genome assembly results with detailed visualizations.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Draft genome assembly presents challenges in ordering contiguous sequences (contigs).
- Accurate contig ordering is crucial for reconstructing complete genomes.
Purpose of the Study:
- To introduce Mauve Contig Mover, a novel software tool for ordering draft genome contigs.
- To leverage comparative genomics for improved genome assembly.
Main Methods:
- Utilizing the Mauve aligner and viewer for sequence alignment.
- Implementing an automated reordering algorithm based on reference genome comparisons.
- Developing a drill-down display for detailed analysis of contig order.
Main Results:
- Mauve Contig Mover successfully proposes the relative order of contigs in draft genomes.
- The software facilitates exploration of draft genome assembly results.
Conclusions:
- Mauve Contig Mover provides an effective method for draft genome reordering.
- The tool enhances the analysis of genome assemblies through automated algorithms and visualization.
Related Concept Videos
03:36Genome 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.
01:57Sanger Sequencing
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
03:00Next-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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
02:54Evolutionary 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...