BACKGROUND Epstein-Barr Virus (EBV) has a great co relationship with human malignancies such as gastric carcinoma. Synonymous codon investigations in viruses could help designing vaccine, to generate immunity. Codon Adaptation Index (CAI) has measured translation elongation rate, among the highly expressed genes. The aim of this study was: usage of "CAI" to measure translation efficiency to kno...

A previously employed method that uses the composition of noncoding DNA as the basis of a test for selection between synonymous codons in plastid genes is reevaluated. The test requires the assumption that in the absence of selective differences between synonymous codons the composition of silent sites in coding sequences will match the composition of noncoding sites. It is demonstrated here th...

BACKGROUND Hepatitis E Virus (HEV) is the causative agent of enterically transmitted acute hepatitis and has high mortality rate of up to 30% among pregnant women. Therefore, development of a novel vaccine is a desirable goal. OBJECTIVES The aim of this study was to construct tPAsp-PADRE-truncated open reading frame 2 (ORF2) and truncated ORF2 DNA plasmid, which can assist future studies with...

Human papillomavirus (HPV) is an etiologic agent of the uterine cervix cancer and several other neoplasias in women globally. E6 protein of HPV type 16 is highly conserved and plays the key role in an inducing cancer via suppressing activity of P. We have used different bioinformatics tools for generation of phylogenetic tree, modeling of RNA secondary structure, gene designing and codon optimi...

Recent investigations into the translation termination sites of various organisms have revealed that not only stop codons but also sequences around stop codons have an effect on translation termination. To investigate the relationship between these sequence patterns and translation as well as its termination efficiency, we analysed the correlation between strength of consensus and translation e...

The highly expressed genes database (HEG-DB) is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage fo...

TransTerm-97 contains more than 97 500 non-redundant coding-sequence initiation and termination contexts compiled from GenBank, release 101 (15-June-1997). In addition, several coding sequence parameters are available: coding sequence length, Nc, GC3, and, when it is computable, codon adaptation index (CAI). Codon usage tables and summaries of start and stop codon contexts are also included. Th...

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the...

UNLABELLED The Codon Adaptation Index (CAI) was introduced by Sharp and Li in 1987 to quantify codon usage similarities between a coding sequence and a set of reference sequences. When synonymous codons for a given amino acid exist, highly expressed genes seem to prefer some of them, according to tRNA abundance and thermodynamic issues. Some authors have described CAI-based methods to derive ex...

conclusions by employment of gene optimization strategies, use of viral-based vectors and suppression of plant-derived gene silencing effect, efficient transient expression of hcvcp in tobacco with proper antigenic properties could be possible. background hepatitis c virus (hcv) is major cause of liver cirrhosis in humans. hcv capsid (core) protein (hcvcp) is a highly demanded antigen for vario...