The goal of this research is to evaluate the performance of two grammatical inference algorithms in the cleavage site prediction problem both in potyviridae poliprotein sequences and in signal peptides. We plan to compare the performance of our algorithms with other approaches available at this time. Cleavage site prediction is a well known problem in bioinformatics, it consists in predict the ...

Motivation: The importance of non-coding RNAs is becoming increasingly evident, andoften the functionof thesemoleculesdepends on the structure. It is common to use alignments of related RNA sequences to deduce the consensus secondary structure by detecting patterns of co-evolution. A central part of such an analysis is to measure covariation between two positions in an alignment. Here, we rank ...

This chapter gives a graceful introduction to problem of protein threedimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the ‘query’ or ‘target’ sequence. We give an overview of the different classes of modelling techniques, notably template-based and template free. We also discuss the way in which structural pred...

The availability of massive amounts of biological data, distributed in various data sources, has prompted the development of a wide range of data analysis tools. However, due to the heterogeneity and complexity of the domain, performing a specific analysis by combining tools is complicated. In this paper, we argue that the software agent metaphor constitutes a flexible approach towards integrat...

This paper addresses the classification task of data mining (a form of supervised learning) in the context of an important bioinformatics problem, namely the prediction of protein functions. This problem is cast as a hierarchical classification problem. The protein functions to be predicted correspond to classes that are arranged in a hierarchical structure (this takes the form of a class tree)...

Knowing the performance of an application in a Grid environment is an important issue in application development and for scheduling decisions. In this paper we describe the analysis and optimisation of a computationand communication-intensive application from the field of bioinformatics, which was demonstrated at the HPCChallenge of Supercomputing 2002 at Baltimore. This application has been ad...

MOTIVATION Secondary structure prediction of RNA sequences is an important problem. There have been progresses in this area, but the accuracy of prediction from an RNA sequence is still limited. In many cases, however, homologous RNA sequences are available with the target RNA sequence whose secondary structure is to be predicted. RESULTS In this article, we propose a new method for secondary...

MOTIVATION The constraints under which sequence, structure and function coevolve are not fully understood. Bringing this mutual relationship to light can reveal the molecular basis of binding, catalysis and allostery, thereby identifying function and rationally guiding protein redesign. Underlying these relationships are the epistatic interactions that occur when the consequences of a mutation ...

Understanding the structure-function relationship of proteins offers the key to biological processes, and can offer knowledge for better investigation of matters with widespread impact, such as pathological disease and drug intervention. This relationship is dictated at the simplest level by the primary protein sequence. Since useful structures and functions are conserved within biology, a sequ...

Considerable attention has been focused on predicting the secondary structure for aligned RNA sequences since it is useful not only for improving the limiting accuracy of conventional secondary structure prediction but also for finding non-coding RNAs in genomic sequences. Although there exist many algorithms of predicting secondary structure for aligned RNA sequences, further improvement of th...