“One of the most important aspects of this new RNA structure prediction method is that it utilizes an explicit model of sequence evolution.”

The paper deals with a new RNA secondary structure prediction method based on evolutionary analyses, which is in the interesting boundary region between computer science and biology. Classical computer science methods are used to help solve a problem of interest for molecular biologists. This results in a number of citations from both algorithmical and more applied papers. Another reason for our paper being highly cited is that it provides a web-based method for RNA analysis, which is easy to use, and thus fairly widespread.

The method described has helped a number of scientists infer secondary structures for RNA molecules, leading to a new functional understanding. The method has, for example, aided in the determination of the RNA structure of the leader sequence in the HIV genome. The predicted structure has been experimentally verified by the research group of Jørgen Kjems at the University of Aarhus, Denmark. Present experimental work is focusing on the biological importance of these structures.

One of the most important aspects of this new RNA structure prediction method is that it utilizes an explicit model of sequence evolution. By applying this method, it becomes possible to make much more reliable predictions, due to the additional information which can be extracted from related sequences. Including evolutionary information in bioinformatical analyses is a promising approach, often leading to very good results. With the numerous genome projects being undertaken, this additional information is becoming easily available, and good algorithms for its usage are essential.

Chemically, RNA molecules closely resemble DNA, but their biological roles differ significantly. DNA is exclusively used to store information, while most biological functions are undertaken by proteins. RNA has an intermediate role, both participating in the storage and transfer of information and in more directly functional roles.

RNA is involved in a number of the most fundamental cellular processes, including the whole machinery involved in reading the information from DNA sequences and building the encoded proteins. This central role of RNA has led researchers to suggest that RNA may have formed the basis of early life on Earth, before DNA and proteins were used by biological systems.

The function of an RNA molecule is tightly linked to its structure. The biological importance of RNA has of course led many scientists to study the structure and function in great detail. It is, however, a very time-consuming process to experimentally determine the structure. Thus, computational methods, including the one in our paper, have proven very useful in making this research more focused and efficient.