Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New gene prediction method capitalizes on multiple genomes

20.12.2007
Researchers at Stanford University report in the online open access journal, Genome Biology, a new approach to computationally predicting the locations and structures of protein-coding genes in a genome.

Gene finding remains an important problem in biology as scientists are still far from fully mapping the set of human genes. Furthermore, gene maps for other vertebrates, including important model organisms such as mouse, are much more incomplete than the human annotation. The new technique, known as CONTRAST (CONditionally TRAined Search for Transcripts), works by comparing a genome of interest to the genomes of several related species.

CONTRAST exploits the fact that the functional role protein-coding genes play a specific part within a cell and are therefore subjected to characteristic evolutionary pressures. For example, mutations that alter an important part of a protein's structure are likely to be deleterious and thus selected against. On the other hand, mutations that preserve a protein's amino acid sequence are normally well tolerated. Thus, protein-coding genes can be identified by searching a genome for regions that show evidence such patterns of selection. However, learning to recognize such patterns when more than two species are compared has proved difficult.

Previous systems for gene prediction were able to effectively make use of one additional 'informant' genome. For example, when searching for human genes, taking into account information from the mouse genome led to a substantial increase in accuracy. But, no system was able to leverage additional informant genomes to improve upon state-of-the-art performance using mouse alone, although it was expected that adding informants would make patterns of selection clearer. CONTRAST solves this problem by learning to recognize the signature of protein-coding gene selection in a fundamentally different way from previous approaches. Instead of constructing a model of sequence evolution, CONTRAST directly 'learns' which features of a genomic alignment are most useful for recognizing genes. This approach leads to overall higher levels of accuracy and is able to extract useful information from several informant sequences.

... more about:
»CONTRAST »Genome »accuracy »informant »protein-coding

In a test on the human genome, CONTRAST exactly predicted the full structure of 59% of the genes in the test set, compared with the previous best result of 36%. Its exact exon sensitivity of 93%, compared with a previous best of 84%, translates into many thousands of exons correctly predicted by CONTRAST but missed by previous methods. Importantly, CONTRAST's accuracy using a combination of eleven informant genomes was significantly higher than its accuracy using any single informant. The substantial advance in predictive accuracy represented by CONTRAST will further efforts to complete protein-coding gene maps for human and other organisms.

Further information about existing gene-prediction methods and the advance CONTRAST brings to the field can be found in a minireview by Paul Flicek, which accompanies the article by Batzoglou and colleagues.

Charlotte Webber | alfa
Further information:
http://genomebiology.com/
http://www.biomedcentral

Further reports about: CONTRAST Genome accuracy informant protein-coding

More articles from Life Sciences:

nachricht Rutgers scientists discover 'Legos of life'
23.01.2018 | Rutgers University

nachricht Researchers identify a protein that keeps metastatic breast cancer cells dormant
23.01.2018 | Institute for Research in Biomedicine (IRB Barcelona)

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Optical Nanoscope Allows Imaging of Quantum Dots

Physicists have developed a technique based on optical microscopy that can be used to create images of atoms on the nanoscale. In particular, the new method allows the imaging of quantum dots in a semiconductor chip. Together with colleagues from the University of Bochum, scientists from the University of Basel’s Department of Physics and the Swiss Nanoscience Institute reported the findings in the journal Nature Photonics.

Microscopes allow us to see structures that are otherwise invisible to the human eye. However, conventional optical microscopes cannot be used to image...

Im Focus: Artificial agent designs quantum experiments

On the way to an intelligent laboratory, physicists from Innsbruck and Vienna present an artificial agent that autonomously designs quantum experiments. In initial experiments, the system has independently (re)discovered experimental techniques that are nowadays standard in modern quantum optical laboratories. This shows how machines could play a more creative role in research in the future.

We carry smartphones in our pockets, the streets are dotted with semi-autonomous cars, but in the research laboratory experiments are still being designed by...

Im Focus: Scientists decipher key principle behind reaction of metalloenzymes

So-called pre-distorted states accelerate photochemical reactions too

What enables electrons to be transferred swiftly, for example during photosynthesis? An interdisciplinary team of researchers has worked out the details of how...

Im Focus: The first precise measurement of a single molecule's effective charge

For the first time, scientists have precisely measured the effective electrical charge of a single molecule in solution. This fundamental insight of an SNSF Professor could also pave the way for future medical diagnostics.

Electrical charge is one of the key properties that allows molecules to interact. Life itself depends on this phenomenon: many biological processes involve...

Im Focus: Paradigm shift in Paris: Encouraging an holistic view of laser machining

At the JEC World Composite Show in Paris in March 2018, the Fraunhofer Institute for Laser Technology ILT will be focusing on the latest trends and innovations in laser machining of composites. Among other things, researchers at the booth shared with the Aachen Center for Integrative Lightweight Production (AZL) will demonstrate how lasers can be used for joining, structuring, cutting and drilling composite materials.

No other industry has attracted as much public attention to composite materials as the automotive industry, which along with the aerospace industry is a driver...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

10th International Symposium: “Advanced Battery Power – Kraftwerk Batterie” Münster, 10-11 April 2018

08.01.2018 | Event News

See, understand and experience the work of the future

11.12.2017 | Event News

Innovative strategies to tackle parasitic worms

08.12.2017 | Event News

 
Latest News

Rutgers scientists discover 'Legos of life'

23.01.2018 | Life Sciences

Seabed mining could destroy ecosystems

23.01.2018 | Earth Sciences

Transportable laser

23.01.2018 | Physics and Astronomy

VideoLinks Science & Research
Overview of more VideoLinks >>>