In recent years, the whole genome sequencing projects of the human species and several other species have produced large amounts of raw sequence data. This consists of the establishment of DNA sequence of four bases (A, C, G and T). A genome contains DNA, which in turn contains the genetic information of an organism – in other words, instructions as to what the organism is like.
Virpi Ahola studied the protein sequence alignments of various species. The aim is to align the sequences of different species on top of each other so that the evolutionally, structurally or functionally corresponding positions of sequences appear in the same column. The length of the alignments varies from 50 or so to thousands of amino acids.
BASIC RESEARCH FOR MANY DIFFERENT DISCIPLINES
Nowadays, the alignments are performed with computer software. Virpi Ahola explains that this constitutes basic research that can be used in nearly all of the applications of molecular genomics, e.g. in medical and pharmaceutical research, plant and animal breeding, in food research and the conservation of animal and plant genetic resources.
“It is important to strive for maximal accuracy in the alignments, in order to prevent mistakes in the analysis in its early stages,” stresses Ahola.
The statistical method that she has developed predicts the likelihood of matching the same positions of proteins from different species. “Even though arranging sequences of letters on top of each other may seem easy, performing the alignments is actually a highly demanding task. No comprehensive mathematical or computational solution has so far been found for the problem of aligning multiple sequences,” comments Ahola.
MANY NEW IDEAS FOR METHODOLOGY
The biological relevance of the method developed by Virpi Ahola is verified by quality control. This is achieved with the help of databases providing biologically plausible alignments. In her study, Ahola realigned these sequences. The new alignments were then compared to the alignments provided by the database with the method described in the thesis. The result of the calculation was then tested by comparing it to the “true” quality of the alignment.
“The results show that my method can be used to reliably predict the quality of alignments,” Virpi Ahola concludes.
In her doctoral thesis, Ahola introduces a method that can be used to locate functionally and structurally important sites of proteins.
The doctoral thesis in Statistics “Statistical methods for conservation and alignment quality in proteins” by Virpi Ahola (MSocSc) will be cross-examined at the University of Turku on 7 November 2008. The opponent is Professor Arne Elofsson from Sweden and the custodian Professor Esa Uusipaikka.
For more information, please contact: Virpi Ahola, MTT Agrifood Research Finland, email@example.com , +358 (0)3 4188 3202
Ulla Jauhiainen | alfa
New study shows producers where and how to grow cellulosic biofuel crops
17.01.2018 | University of Illinois College of Agricultural, Consumer and Environmental Sciences
Robotic weeders: to a farm near you?
10.01.2018 | American Society of Agronomy
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...
What enables electrons to be transferred swiftly, for example during photosynthesis? An interdisciplinary team of researchers has worked out the details of how...
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...
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...
Scientists at Tokyo Institute of Technology (Tokyo Tech) and Tohoku University have developed high-quality GFO epitaxial films and systematically investigated their ferroelectric and ferromagnetic properties. They also demonstrated the room-temperature magnetocapacitance effects of these GFO thin films.
Multiferroic materials show magnetically driven ferroelectricity. They are attracting increasing attention because of their fascinating properties such as...
08.01.2018 | Event News
11.12.2017 | Event News
08.12.2017 | Event News
19.01.2018 | Materials Sciences
19.01.2018 | Health and Medicine
19.01.2018 | Physics and Astronomy