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Comparative Genomics

Genome Differences in Plain View

Comparing two or more genomes is fast and easy with Whole Genome Mapping (WGM) technology and advanced analysis tools. The maps allow you to see and compare genomic content with higher accuracy across the entire genome.

Even highly related organisms can be accurately analyzed to confirm the similarities and locate regions that are different (Figure 1). These differences can be challenging to detect due to complex genomic variation or mobile elements. Using in silico restriction maps in comparisons, the WGM technology can determine the presence or absence of annotated genes by discovering the regions displaying alignment of restriction patterns (Figure 2).

Find genetic variation: insertions, deletions and other genetic modifications
Track mobile elements including pathogenicity islands, phage and transposons
Differentiate strains and genetic relatedness between multiple isolates

Figure 1. P. aeruginosa ATCC 27317 compared to sequenced Liverpool epidemic strain LESB58.Prophages and genomic islands (LESGI) identified in the sequenced isolate are indicated (red). Closer examination of prophage 3 locus (Detailed view) indicates absence of the prophage in ATCC 27317.

Figure 2. Large insertion detected in multi-drug resistant strain (red rectangle)

OpGen provides proprietary software called MapSolver™ to analyze the sequences and compare maps with a high level of accuracy. You can take advantage of Whole Genome Mapping and high definition analysis with a MapIt Service map analysis of your samples. Or you can bring the Argus Whole Genome Mapping System into your lab to process samples and analyze multiple-map comparison and cluster analysis.

“Physical map and genetic map still should be emphasized as an important parts of a reference genome. Recent progress in technologies, such as the whole genome mapping high-throughput platform offered by OpGen, now provide the tools for efficient physical map construction. This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing. We applied this technology as an assistant tool of the NGS to assemble bacterial, plant and large mammalian genome with reliable accuracy and generate the sub-chromosome graded assembly. The experience in these genome assembly projects shows that the physical map should be the standard for any reference genome to be assembled in further.”

Xun Xu, Ph.D.

Deputy Director at BGI

This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing.

Xun Xu, Ph.D.
Deputy Director at BGI

“Our research focuses on a wide variety of projects from viruses and microbes to crop plants and mammals. Many of our projects are de novo assembly projects, where, without a closely related genome sequence, it can be difficult to critically assess the results. We often combine different sequencing technologies, and we are finding that regardless of the sequencing platform, error correction, or assembler used, OpGen’s Whole Genome Mapping identifies misassemblies and provides the highest quality de novo assembly for further research.”

Matthew Clark, Ph.D.

Team Leader, Sequencing Technology Development

The Genome Analysis Centre (TGAC), Norwich, UK

OpGen’s Whole Genome Mapping identifies misassemblies and provides the highest quality de novo assembly for further research.

Matthew Clark, Ph.D.
Team Leader, Sequencing Technology Development

“We adopted OpGen’s Argus System as the most advanced way of adding Whole Genome Mapping to improve whole genome sequences. We combined Whole Genome Maps with sequence assemblies to correct errors and misassemblies in bacterial genome sequences as part of our program in the Human Microbiome Project. We are now moving the technology into larger genome projects.” 

George Weinstock, Ph.D.

Associate Director  The Genome Institute at Washington University

We combined Whole Genome Maps with sequence assemblies to correct errors and misassemblies in bacterial genome sequences. This is part of our program from the Human Microbiome Project.

George Weinstock Ph.D.
 Associate Director 
The Genome Institute at Washington University

“Certain things you just have a tough time answering with de novo sequencing. And assembly doesn’t always work out as sweetly as you would like. So definitely for any whole genome de novo project that people are insistent on closing we would do a Whole Genome Map optically as well as de novo assembly. And the amount of money you would save is in the thousands of dollars in finishing.”

Stefan Green

Director of DNA Services

University of Illinois Chicago Research Resources Center (UIC RRC)

Definitely for any whole genome de novo project that people are insistent on closing we would do a Whole Genome Map.

Stefan Green
Director of DNA Services