Background Human coagulation factor IX is a 57kDa plasma serine protease made in Liver which plays a vital role in the blood coagulation cascade. FIX deficiency causes severe disorder Hemophilia B or Christmas disease. Nowadays, recombinant proteins have important roles in treatment of diseases. Although, cultivated mammalian cells because of their ability for producing properly folded protein ...

The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selectio...

Codon Optimization helps increasing immuno-stimulatory nucleotide motifs or decreasing immunesuppresive motifs in DNA expression vectors. This enhances the efficiency of DNA vaccinations. In this paper, we investigate the existing Pattern Matching algorithm for Codon Optimization and try to rewrite the algorithm in MapReduce programming model for execution speed-up and faster computation. Keywo...

Protein purification is not a simple task. Yet, overexpression at bacterial systems with recombinant modifications brings further difficulties. Adding tag, an affinity label, and expressing particular domains of the whole protein, especially hydrophobic sections, make challenging process. folding pattern may perturb N- or C-terminal tag this terminal preference lead to poor yield. Codon optimiz...

results escherichia coli phytase was expressed in p. pastoris under different cultivation conditions (post-induction temperature, methanol concentration, and post-induction ph). the optimized conditions by rsm using face centered central composite design were 1% (v/v) methanol, ph = 5.8, and 24.5°c. under the optimized conditions, appa was successfully expressed in p. pastoris and the maximum p...

Translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of tRNAs in the ribosomal A- and P-sites. Here, we sought evidence of A- and P-site tRNA interaction by examining bias in codon pair choice within open reading frames from a range of genomes. Three distinct and marked effects were revealed once codon and dipeptide biases had been subtracted. First, i...

SUMMARY Codon optimization has been widely used for designing synthetic genes to improve their expression in heterologous host organisms. However, most of the existing codon optimization tools consider a single design criterion and/or implement a rather rigid user interface to yield only one optimal sequence, which may not be the best solution. Hence, we have developed Codon Optimization OnLine...

Typically, work on preference elicitation and reasoning about preferences has focused on the problem of specifying, modeling, and optimizing with preference over outcomes corresponding to single objects of interest. In a number of applications, however, the “outcomes” of interest are really sets of such atomic outcomes. For instance, when trying to form coalitions or committees, we need to sele...

Dengue is the most common arthropod-borne viral (Arboviral) illness in humans. The genetic features concerning the codon usage of dengue virus (DENV) were analyzed by the relative synonymous codon usage, the effective number of codons and the codon adaptation index. The evolutionary distance between DENV and the natural hosts (Homo sapiens, Pan troglodytes, Aedes albopictus and Aedes aegypti) w...