# Web-based visualization of coronavirus genomes and proteins

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA BERKELEY · 2020 · $354,767

## Abstract

Project Summary
This supplemental proposal knits together several bioinformatics
visualization tools in the service of SARS-CoV-2 genome analysis.
The core of the proposal is a newly-prototyped JavaScript viewer,
ABrowse, that is capable of rendering multiple sequence alignments,
navigable by phylogenetic trees, and integrated with protein structure
views, all in a single embeddable component. The ABrowse viewer is
currently employed to render the Pfam SARS-CoV-2 special release:
a collection of 40 protein domains from the coronavirus genome, along
with PDB structures. (ABrowse is also a candidate for Pfam's future
default viewer, as noted in the letters of support.)
We propose to accelerate ABrowse development for use by the
COVID-19 pandemic, specifically targeting scaling, performance, and
integration issues that are most relevant to scientists studying the
virus. Chief amongst these is scaling ABrowse to handle millions of
protein sequences (and/or SARS-CoV-2 genome sequences) by
means of a new, compressed storage format suitable for
random-access user-driven exploration of very large trees (and
alignments) over the web.
Beyond scaling, we also address integration, developing plugins for
ABrowse to run within JBrowse (the genome browser that is the focus
of the project to which this is a supplemental proposal) as well as
Auspice (the web dashboard of NextStrain, the phylogenetic genome
alignment and annotation package that is widely used for COVID-19
analysis). We also propose several user interface enhancements to
make ABrowse more useful as a navigation tool for COVID-19 data.

## Key facts

- **NIH application ID:** 10162044
- **Project number:** 3R01HG004483-12S1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA BERKELEY
- **Principal Investigator:** Ian H Holmes
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $354,767
- **Award type:** 3
- **Project period:** 2020-09-04 → 2021-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10162044

## Citation

> US National Institutes of Health, RePORTER application 10162044, Web-based visualization of coronavirus genomes and proteins (3R01HG004483-12S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10162044. Licensed CC0.

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