The need for accurate, automated protein classification methods continues to increase as advances in biotechnology uncover new proteins. G-protein coupled receptors (GPCRs) are a particularly difficult superfamily of proteins to classify due to extreme diversity among its members. Previous comparisons of BLAST, k-nearest neighbor (k-NN), hidden markov model (HMM) and support vector machine (SVM...

background: avian infectious bronchitis (ib), with avianinfectious bronchitis virus (ibv) as the causing agent, is a ubiquitous endemicdisease of the chicken with devastating effects on its industry. a viralmembrane surface protein called s  notonly induces neutralizing antibodies but also plays an important role in virusbinding and entry to host cells. technically, s1 protein gene sequencing a...

Background: Avian infectious bronchitis (IB), with avianinfectious bronchitis virus (IBV) as the causing agent, is a ubiquitous endemicdisease of the chicken with devastating effects on its industry. A viralmembrane surface protein called S  notonly induces neutralizing antibodies but also plays an important role in virusbinding and entry to host cells. Technically, S1 protein gene sequencing a...

Motivation: Position-specific scoring matrices have been used extensively to recognize highly conserved protein regions. We present a method for accelerating these searches using a suffix tree data structure computed from the sequences to be searched. Methods: Building on earlier work that allows evaluation of a scoring matrix to be stopped early, the suffix tree-based method excludes many prot...

Preface This study was completed as a master thesis at the institute of Informatics and Mathematical Modeling (IMM)-Technical University of Denmark (DTU). The project has been completed in the period between September 1 st 2003 and Marts 1 st 2004 (and is rated as 35 points). Associate Professor Paul Fischer also IMM, DTU has been supervisor for the project. The report deals with a general clas...

The laborious, and cost-inefficient biochemical methods for identifying thermophilic proteins necessarily require a rapid accurate method proteins. Recently, machine learning has become more effective specific classes of extremophiles. There is still need low-cost proteins, despite the fact that studies employing yielded superior results to conventional methods. Here, we avoid problem manually ...

Discovering new biological knowledge from the highthroughput biological data is a major challenge to bioinformatics today. To address this challenge, we developed a new approach for protein classification. Proteins that are evolutionarilyand thereby functionallyrelated are said to belong to the same classification. Identifying protein classification is of fundamental importance to document the ...