Eliciting the preferences of a decision maker is a crucial step when applying multi-criteria decision aid methods on real applications. Yet it remains an open research question, especially in the context of the Promethee methods. In this paper, we propose a bi-objective optimization model to tackle the preference elicitation problem. Its main advantage over the widely spread linear programming ...

Synonymous codon choices at the beginning of genes optimize 5' RNA structures for enhanced translation initiation, but less is known about mechanisms that drive codon optimization downstream within the gene. To understand what determines codon choices across a gene, we generated 12,726 in situ codon mutants in the Escherichia coli essential gene infA and measured their fitness by combining mult...

for high-throughput production of recombinant protein in escherichia coli ( e. coli ), besides important parameters such as efficient vector with strong promoter and compatible host, other important issues including codon usage, rare codons, and gc content specially at n-terminal region should be considered. in the current study, the effect of decreasing the percentage of gc nucleotides and opt...

The relationship between the selection affecting codon usage and selection on protein sequences of orthologous genes in diverse groups of bacteria and archaea was examined by using the Alignable Tight Genome Clusters database of prokaryote genomes. The codon usage bias is generally low, with 57.5% of the gene-specific optimal codon frequencies (Fopt) being below 0.55. This apparent weak selecti...

TCP-nets are a popular approach within the AI community for preference handling. Concurrently, within the database community lots of work has been done to integrate preference handling into database query languages like Preference SQL, building on a variety of preference constructors under a strict partial order semantics. Moreover, many sophisticated algebraic optimization techniques and prefe...

The imperfect fungus, Candida albicans is the major yeast pathogen in humans (1). We have analysed the codon usage in eleven C. albicans gene sequences reported in the EMBL and GenBank databases (Table). The codons are divided into three groups (low, medium and high) based upon their codon usage (Table), and these groups are compared with analogous groups for the highly expressed genes from S. ...

Most organisms use different mechanisms of translation termination for the three types of stop codons, i.e. UAA, UAG, and UGA [1]. Using the GenBank database, we have conducted comprehensive computer analyses of translation termination sites in order to find the difference of consensus sequence patterns around each type of stop codons. We also systematically analyzed the preference of stop codo...

Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes f...

Shaanxi Province, China Hemoglobin is a protein responsible for the transport of oxygen. The preference of hemoglobin coding gene is analyzed by CodonW. The relationship between the A3 / (A3 + T3) and G3 / (G3 + C3) and the relationship between GC12 and GC3 are all investigated. Finally, the preference of hemoglobin coding gene is shown and discussed. The results show that codon use preference ...