Feeds

Algorithm ramps up genetic computation

'Sailfish' boosts RNA gene expression predictions

Application security programs and practises

The world has built DNA genomes for a long time, but applying what we know about genetics to everyday medicine is a tough ask.

For example, readers might remember that the business of crafting treatments from genes is so complex that IBM recently entered a partnership to get its Watson megabrain learning to help medicos craft personalised treatments for cancer.

Part of the problem that researchers want to solve is “gene expression”: in all the complexities of how genes interact, what interactions are “expressed” in a physical trait? – whether that trait is blue eyes, or why one individual dies of a cancer that's arrested in someone else.

What's wanted is a way to predict gene expression, and one angle of the research is based on RNA sequencing (RNA-seq) data. The problem is that analysing RNA sequencing is a slow business, and that's where the research out of Carnegie-Mellon University and the University of Maryland comes in. Their Sailfish algorithm dramatically accelerates estimates of the likely outputs of RNA sequence.

To explain why this is important, the researchers' release says: “Though an organism's genetic makeup is static, the activity of individual genes varies greatly over time, making gene expression an important factor in understanding how organisms work and what occurs during disease processes. Gene activity can't be measured directly, but can be inferred by monitoring RNA, the molecules that carry information from the genes for producing proteins and other cellular activities.”

However, analysing the RNA-seq “reads” – short sequences of RNA – traditionally results in huge datasets that have to be mapped back to their original genetic processes. The Sailfish “secret sauce” (except that it's not so secret – the code has been released here) is that it skips this painstaking mapping step.

Instead, the researchers “found they could allocate parts of the reads to different types of RNA molecules, much as if each read acted as several votes for one molecule or another”. Think of it as upvoting posts in a forum: individual votes bestow a kind of consensus on which reads – or posts – carry the greatest significance.

Getting what might be a 15-hour analysis down to minutes is important, the researchers believe: there are already huge repositories of RNA-seq data, but turning data into insight is held back by computational effort.

Fifteen hours for each analysis “really starts to add up, particularly if you want to look at 100 experiments”, explains Carnegie-Mellon associate professor Carl Kingsford. “With Sailfish, we can give researchers everything they got from previous methods, but faster.” ®

Build a business case: developing custom apps

More from The Register

next story
Asteroid's DINO KILLING SPREE just bad luck – boffins
Sauricide WASN'T inevitable, reckon scientists
BEST BATTERY EVER: All lithium, all the time, plus a dash of carbon nano-stuff
We have found the Holy Grail (of batteries) - boffins
The Sun took a day off last week and made NO sunspots
Someone needs to get that lazy star cooking again before things get cold around here
Boffins discuss AI space program at hush-hush IARPA confab
IBM, MIT, plenty of others invited to fill Uncle Sam's spy toolchest, but where's Google?
Famous 'Dish' radio telescope to be emptied in budget crisis: CSIRO
Radio astronomy suffering to protect Square Kilometre Array
Bad back? Show some spine and stop popping paracetamol
Study finds common pain-killer doesn't reduce pain or shorten recovery
prev story

Whitepapers

Implementing global e-invoicing with guaranteed legal certainty
Explaining the role local tax compliance plays in successful supply chain management and e-business and how leading global brands are addressing this.
Consolidation: The Foundation for IT Business Transformation
In this whitepaper learn how effective consolidation of IT and business resources can enable multiple, meaningful business benefits.
Application security programs and practises
Follow a few strategies and your organization can gain the full benefits of open source and the cloud without compromising the security of your applications.
How modern custom applications can spur business growth
Learn how to create, deploy and manage custom applications without consuming or expanding the need for scarce, expensive IT resources.
Securing Web Applications Made Simple and Scalable
Learn how automated security testing can provide a simple and scalable way to protect your web applications.