# The UCSC Genome Browser

> **NIH NIH U41** · UNIVERSITY OF CALIFORNIA SANTA CRUZ · 2020 · $1,385,782

## Abstract

This component describes our plans to develop, maintain, and extend the UCSC Genome Browser software,
build and maintain genome browsers and annotations for species of biomedical interest, and integrate data
from the scientific community that help interpret the functions of various genome regions.
The UCSC Genome Browser has met the needs of the genomics and biomedical communities for over sixteen
years while accommodating a dramatic increase in the volume of data and simultaneous users, supporting a
wealth of new data types, and adapting to new computing platforms and displays. Our web-based tools garner
over one million hits per day, and our Unix command-line tools are used in genomic analysis pipelines
throughout the world. During the upcoming period we plan to expend more effort on maintaining and extending
the Genome Browser software than on any other aim in this proposal. Highlights of our planned work include
adding new displays to interpret personal genomes, developing displays that aggregate the increasing volumes
of data, adding visualization support for chromatin conformation capture data and other data that cannot be
easily shown in a linear, two-dimensional chromosome view, improving search capabilities of our databases
and hubs, building a version targeted at mobile devices, and building browsers and displays that support single
cell data.
The Genome Browser database offers genomic data for nearly 100 organisms, many with multiple assemblies.
The human and mouse genomes, which include the most recent assemblies from the Genome Reference
Consortium, are the most richly annotated. We will continue to import new and updated assemblies, focusing
on vertebrate genomes and with an emphasis on primates, animals used in scientific research, and animals
that help extend coverage of the vertebrate phylogenetic tree. We intend to make it easier to build browsers
and related tools on new genomes, automating the process when possible. We plan to map and compute
annotations on patches issued between major releases of the human and mouse genomes to increase the
usefulness of the patches to the scientific community. We will periodically evaluate multiple genome alignment
software in search of a superior alternative to our existing pipeline.
The genome framework is an ideal platform for integrating the research findings of a broad range of scientists.
We plan to continue importing new data releases from projects that we currently support, in particular the
GTEx and ENCODE projects, as well as incorporating new data from selected projects and papers
recommended to us by our users, our scientific advisory board, and our funding agency. We will encourage the
use of track hubs by external project groups and consortia for displaying their data sets in the browser. We
also plan to integrate de-identified data into our public browser, and will coordinate with dbGAP to allow their
authorized users to access specific, identifiable, private data sets in a sec...

## Key facts

- **NIH application ID:** 9969402
- **Project number:** 5U41HG002371-21
- **Recipient organization:** UNIVERSITY OF CALIFORNIA SANTA CRUZ
- **Principal Investigator:** William James Kent
- **Activity code:** U41 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $1,385,782
- **Award type:** 5
- **Project period:** 2001-07-12 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9969402

## Citation

> US National Institutes of Health, RePORTER application 9969402, The UCSC Genome Browser (5U41HG002371-21). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9969402. Licensed CC0.

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