Dot: An Interactive Dot Plot Viewer for Comparative Genomics

Author: Maria Nattestad, Scientific Visualization Lead

 

 

 

Introduction

Next week, DNAnexus will be at the Plant and Animal Genome conference (PAG) in San Diego (booth 431). As part of an ongoing effort to expand our visualization capabilities, we will present an open-source tool called Dot that helps scientists visualize genome-genome alignments through a rich, interactive dot plot.

In addition to its scientific contribution, Dot encourages community development of new visualization tools by providing a template that can be used for new visualization tools in other areas of bioinformatics. This would allow bioinformaticians to focus on the bioinformatics and visualization without needing to master web programming intricacies such as reading data from local and remote servers, which is all handled by Dot’s modular and reusable inner workings.

Importance of Dot Plots

Constructing a genome assembly is fundamental to studying the biology of a species. In recent years, advances in long-read sequencing and scaffolding technologies have led to unprecedented quality and quantity of genome assemblies. Better reference genomes contribute to better gene annotations, evolutionary understanding, and biotech opportunities.

Comparing new assemblies to existing genomes of related species is crucial to understanding differences between organisms across the tree of life. Genome assemblies are never perfect and always have to be evaluated critically by comparing against other assemblies or reference genomes, whether of the same or a closely related species. Comparative genomics is also how assemblies of two species’ genomes can be compared and contrasted to look for features that represent functional differences or inform the study of their evolution.

The classic method for visualizing genome-genome alignments is the dot plot, which provides an excellent overview of alignments from the perspective of both genomes. Dot plots place the reference genome on one axis and the query genome (that is aligned against the reference) on the other axis. Alignments between the two genomes are placed according to their coordinates on both genomes. Whereas genome browsers (such as IGV and the UCSC Genome Browser) plot data in one dimension on one genome, dot plots use two dimensions to show alignments in two genomes’ coordinates spaces simultaneously. This is necessary when representing large genome alignment data where the query coordinates matter just as much as the reference coordinates for a particular alignment.

However, dot plots have barely changed in the past decade and are still generated from the command-line as static images, limiting detailed investigation. We decided to tackle this problem as an open-source science project at DNAnexus.

Introducing Dot

Here we present Dot, an interactive dot plot viewer that allows genome scientists to visualize genome-genome alignments in order to evaluate new assemblies and perform exploratory comparative genomics.

Dot supports the output of MUMmer’s nucmer aligner the most commonly used software method for aligning genome assemblies. A quick script called DotPrep.py converts the delta file to a more streamlined coordinates file with an index that enables Dot to read in more alignments in certain regions on demand.

Interactivity and features

Dot adds a number of useful features on top of the classic dot plot concept. The index enables a quick plot of an overview that includes the longest 1000 alignments. From here, users can zoom in to look at particular regions and load all the alignments for regions of interest.

In addition to showing alignments, Dot allows scientists to load annotations for either or both genomes to show additional context  (e.g. understanding how sequence differences map to gene differences). Annotation tracks are a common feature of one-dimensional genome browsers, but to translate this concept to the two-dimensional dot plot, we enable annotation tracks on both axes. This is a major benefit of Dot that makes it possible to compare gene annotations visually alongside the alignments of the DNA sequences.

Moreover, users can jump to the same region of the reference genome in the UCSC Genome Browser to quickly see additional context for a region of interest. This allows scientists to explore how known repetitive elements in the reference genome could potentially affect assembly quality in specific regions.

Details for developers

By leveraging D3 and canvas in JavaScript, Dot combines the benefits of interactivity with scalability, enabling scientists to explore large genomes. The UI on the right side panel is built using an open-source SuperUI.js [https://github.com/marianattestad/superui] plugin, and the input handling and basic page navigation is set up through a special VisToolTemplate [https://github.com/MariaNattestad/VisToolTemplate] plugin we developed to enable others to create new visualization tools more easily. We encourage developers to utilize and build on Dot and these open-source projects to create their own visualization tools. Dot is very modular and can be used as a template to build new visualization tools. The template handles complex and necessary components like reading input data files from various sources, thereby letting developers focus only on the visualization itself.

Dot is open source

Dot is free to use online at [https://dnanexus.github.io/dot/] and open source at [https://github.com/dnanexus/dot]. For DNAnexus users, there is a package available among the featured projects with (1) an applet for running MUMmer’s nucmer aligner that includes DotPrep.py, (2) a shortcut  to Dot to send files from DNAnexus quickly, and (3) example data and results.

 

PAG 2018: A Focus on Genome Assembly

The DNAnexus team is headed to San Diego, January 13-17, for the largest gathering of Ag-Genomics scientists in the world! The International Plant & Animal Genome Conference brings together over 3,000 leading genomic scientists in plant and animal research to discuss recent advancements, ongoing projects, and future studies in the field. Learn more about PAG and register here.

Visit DNAnexus in booth #431 to learn how we can be your partner for complex genome assembly, structural variation analysis, and physical mapping to achieve complete and accurate views of all types of genomic variation. Join our activities listed below, or email us to schedule a member of our team at the conference.

Demo Hour with PacBio

Transforming De Novo Assembly
Tuesday, January 16th, 10:00am-10:30am
DNAnexus Booth #431

Stop by our booth to learn how to leverage PacBio’s FALCON and FALCON-Unzip tools on DNAnexus for streamlined genome assembly. Bioinformaticians from PacBio and DNAnexus will be available to answer questions.

DNAnexus Workshops

The Data Backbone for the Vertebrate Genome Consortia
Tuesday, January 16th, 1:30pm-3:40pm
Sunset – Meeting House

Brett Hannigan, PhD, Director of Scientific Partnership, will discuss how the Vertebrate Genomes Project at the Sanger Institute leverages DNAnexus to access approved tools, pipelines, and datasets generated by the consortia.

An Interactive Dot Plot Viewer for Comparative Genomics
Wednesday, January 17th, 11:45am-12:00pm
Digital Tools and Resources Program – California Room

Maria Nattestad, PhD, Scientific Visualization Lead, will debut Dot, our interactive dot plot viewer that enables scientists to visualize genome-genome alignments in order to evaluate new assemblies and perform explorative comparative genomics.

Dot will also be presented as a poster (PO104) Monday, January 15th from 10:00am-11:30am in the Grand Exhibit Hall.

CIO Webinar Series: Genomic Data Privacy in the Cloud

Join our two-part webinar series focusing on infrastructure requirements to scale geno-pheno analysis and realize genomic-based clinical trials. Can’t make it? Register anyway and we’ll send you the recording.

Advances in DNA sequencing have created tremendous volumes of whole-genome sequence and multi-omics data, creating new opportunities to explore how the genome plays a role in human disease. As the use of human genomic information becomes more prevalent in research and clinical care, it is important to understand the responsibilities for handling of data in these contexts. The inclusion of genomic information has also shown reduction in costs and time, and improved results of clinical trials. The reduction in sequencing costs and increasing value of NGS in clinical trials is leading some organizations to incorporate NGS into the majority of their trials.

Webinar 1: Understanding Security, Privacy, and the Regulatory Landscape for Genomics in Research and Clinical Settings
January 23rd, 2018
10:00am PST/1:00pm EST

Loren Buhle, PhD, VP Security, Quality & Compliance
Loren is a seasoned leader with over three decades of experience working in the regulated space of life sciences, clinical, and basic research. He brings an unusual combination of scientific, commercial, regulatory, quality, and IT disciplines to identify and manage security, quality, and compliance issues. 

 

Webinar 2: Major IT Considerations for Genomics in Healthcare
February 28th, 2018
10:00am PST/1:00pm EST

Omar Serang, Chief Cloud Officer
Omar has decades of experience building global operations teams and infrastructures, including cloud computing at Amazon Web Services, social web real-time analysis services at Topsy Labs, and messaging and messaging security services at Cloudmark and Critical Path. 

 

 

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