Categories: Science & Environment

“Google for DNA” brings order to biology’s big data

MetaGraph index and extensive archives of DNA, RNA and protein sequences. Scientists can search archives and trace biological contexts in Big Data.Credit: Andrew Brookes/Connect Images/Scientific Photo Library

Internet has Google. Now biology has MetaGraph. Detailed today in Nature1the search engine can quickly sift through the impressive volumes of biological data housed in public repositories.

“It’s a huge achievement,” says Rayan Chikhi, a bioinformatics researcher at the Pasteur Institute in Paris. “They set a new standard” for analyzing raw biological data – including DNA, RNA and protein sequences – from databases that can contain millions of billions of DNA letters, representing “petabases” of information, or more entries than all the web pages in Google’s vast index.

Although MetaGraph is labeled “Google for DNA,” Chikhi likens the tool to a search engine for YouTube because the tasks are more computationally demanding. In the same way that YouTube searches can retrieve every video featuring, say, red balloons, even when those keywords don’t appear in the title, tags, or description, MetaGraph can uncover genetic patterns hidden deep within a large sequencing dataset without needing those patterns to be explicitly annotated in advance.

“It allows things that couldn’t be done otherwise,” says Chikhi.

Indexing the Library of Life

The motivation behind MetaGraph was to solve an accessibility problem in sequencing datasets. The size of these repositories has grown at a rapid pace in recent decades, but this growth has presented challenges to scientists who use the data they contain. Raw sequencing reads are fragmented, noisy, and too numerous to search directly. “Paradoxically, the volume of data is the main obstacle to its use,” explains Babaian.

According to study author André Kahles, a bioinformatician at the Swiss Federal Institute of Technology Zurich (ETH) in Switzerland, MetaGraph could help researchers ask biological questions of repositories such as the Sequence Read Archive (SRA), a public database containing more than 100 million billion letters of DNA.2

They approached the problem using mathematical “graphs” that connect overlapping DNA fragments, much like sentences sharing the same words lined up in a book index.

The researchers integrated data from seven publicly funded data repositories, creating 18.8 million unique sets of DNA and RNA sequences and 210 billion sets of amino acid sequences across all groups of life, including viruses, bacteria, fungi, plants and animals, including humans. They also developed a search engine for these sequences, in which users use text prompts to search these embedded archives of raw data.

“It’s a whole new way to interact with this data set,” says Kahles. “It’s compressed, but accessible on the fly.”

To demonstrate the utility of MetaGraph, the study authors used it to analyze 241,384 human gut microbiome samples for genetic indicators of antibiotic resistance around the world, building on work using an earlier version of the tool to track drug resistance genes in bacterial strains that live in the subways of large urban centers.3. The authors claim to have completed the analysis in about an hour on a high-powered computer.

Open road to discovery

Source link

Ethan Davis

Ethan Davis – Science & Environment Journalist Reports on climate change, renewable energy, and space exploration

Recent Posts

NBA annual survey says Thunder will repeat, Nuggets’ Jokic as MVP

Tim BontempsOctober 9, 2025, 11:46 a.m. ETCloseTim Bontemps is a senior NBA writer for ESPN.com who covers the league and…

3 weeks ago

Donald Trump to present Ben Carson with the Presidential Medal of Freedom

Former Secretary of Housing and Urban Development Dr. Ben Carson, recently named National Nutrition Advisor at the U.S. Department of…

3 weeks ago

Federal health insurance premiums will see another significant increase in 2026

Federal employees and annuitants are heading into another year of sharp increases in their health insurance premiums, both under the…

3 weeks ago

Drake’s Lawsuit Against Kendrick Lamar’s ‘Not Like Us’ Dismissed by Judge

A federal judge on Thursday (Oct. 9) dismissed Drake's defamation lawsuit against Universal Music Group over Kendrick Lamar's "Not Like…

3 weeks ago

10/9: CBS Morning News – CBS News

10/9: CBS Morning News - CBS News Watch CBS News Israel and Hamas agree to first phase of Gaza peace…

3 weeks ago

Letitia James, who sued Trump, indicted for alleged bank fraud: NPR

New York Attorney General Letitia James speaks during a news conference January 8, 2025 in New York. Michael M. Santiago/Getty…

3 weeks ago