"If the parameters are not set to the right values, your model won’t be sound – it won't actually correspond to what you are trying to model." "There are so many different models of scientific phenomena, and they are invariably optimization problems – you are trying to minimize or maximize a function that usually has many parameters whose values need to be set," Kececioglu said.
#BIOLOGICAL SEQUENCE ANALYSIS SOFTWARE#
The underlying approach is remarkably general, and Kececioglu and DeBlasio will make their system available as open source software for widespread use – not merely for those scientists doing biological sequence alignment. "We're automatically finding the configuration that gives a biologist the best results when they run alignment software."įor their work, and the potential of their new techniques, Kececioglu recently received a National Science Foundation grant of nearly $500,000 through September 2015 to advance the technology further. "It's somewhat like setting the configuration in your Internet browser to give yourself the best experience," said DeBlasio, a third-year doctoral student in the computer science department. The newly developed software model is able to quickly analyze those settings, along with information about the sequence provided by the biologist, to swiftly detect the best parameters. With parameter advising, the software Kececioglu and DeBlasio co-developed frees biologists from having to rely on the default settings in the software tools they use for sequence analysis. The aim: to remove the guessing game involved in tuning parameter values, while also improving the ability to obtain the best sequence alignment without having all information available.Īnd there is good news – Kececioglu and one of his graduate students, Dan DeBlasio, have developed a new technique that automatically tunes parameters and improves accuracy by 27 percent using an approach the team has termed "parameter advising." "It's a very common problem: How does a biologist find the right values to use when they run their analysis software? Sometimes you have hundreds of parameters that must be set," said Kececioglu, a UA associate professor of computer science and a BIO5 Institute member. Given that reality, major challenges exist to having accurate results.Īt the University of Arizona, computer scientist John Kececioglu and his collaborators have spent years developing improved computer software to aid biologists in obtaining more accurate analyses. When biologists study proteins, DNA, or other biological molecules that are represented in the computer as sequences, they rely on known information but also must predict missing data. Welcome to the world of computational biologists. Imagine trying to construct a brick building with fewer than the requisite number of bricks and without a detailed blueprint.
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