Background: Little knowledge of synonymous codon usage pattern of pseudorabies virus (PRV) genome, especially the UL31 gene in the process for its evolution is available. Objectives: In the present study, the codon usage bias between PRV UL31 sequence and the UL31-like sequences was identified. Materials and Methods: We used a comprehensive analysi...

Background: The p53 tumor suppressor gene plays important roles in genomic stability. Several reports have noted racial differences in the prevalence of p53 genotypes at the codon 72 in patients with endometriosis.To study the association of endometriosis with p53 codon 72 polymorphism in the population of Isfahan. Materials and Methods: We undertook a case–control study to examine the possible...

The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the origin...

The design and implementation of advanced personalized database applications requires a preference-driven approach. Representing preferences as strict partial orders is a good choice in most practical cases. Therefore the efficient integration of preference querying into standard database technology is an important issue. We present a novel approach to relational preference query optimization b...

We seek to elicit individual design preferences through usercomputer interaction. During an iteration of the interactive session, the computer presents a set of designs to the user who then picks any preferred designs from the set. The computer learns from this feedback and creates the next set of designs using its accumulated knowledge to minimize a merit function. Under the hypothesis that us...

Gene codon optimization may be impaired by the misinterpretation of frequency and optimality of codons. Although recent studies have revealed the effects of codon usage bias (CUB) on protein biosynthesis, an integrated perspective of the biological role of individual codons remains unknown. Unlike other previous studies, we show, through an integrated framework that attributes of codons such as...

We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon pref...

Preference Logic Programming (PLP) is an extension of Constraint Logic Programming (CLP) for declaratively specifying optimization problems. In the PLP framework, the deenite clauses of a CLP program are augmented by two new kinds of clauses: optimization clauses and arbiter clauses. Optimization clauses specify which predicates are to be optimized and arbiter clauses specify the criteria to be...

This paper pursues the idea of a general multiobjective optimizer that can be flexibly adapted to arbitrary user preferences— assuming that the goal is to approximate the Pareto-optimal set. It proposes the Set Preference Algorithm for Multiobjective Optimization (SPAM) the working principle of which is based on two observations: (i) current multiobjective evolutionary algorithms (MOEAs) can be...

The move to relational probabilistic models from propositional models stemmed from the realization that the type of knowledge we have and need in many domains is at a level more generic than that of concrete objects. In reasoning about preference, too, often we have knowledge about the desirable behavior or state of a system of agents/objects, that applies to different instantiations of this sy...