conclusions based on the location of detected rccs in the structure of hbv proteins, it was found that these rccs may have a critical role in correct folding of hbv proteins and can be considered as drug targets. the results of this study provide new and deep perspectives about structure of hbv proteins for further researches and designing new drugs for treatment of hbv. results the pfam search...

background recent studies suggest that rare codon clusters are functionally important for protein activity. methods here, for the first time we analyzed and reported rare codon clusters in hepatitis c virus (hcv) genome and then identified the location of these rare codon clusters in the structure of hcv protein. this analysis was performed using the sherlocc program that detects statistically ...

BACKGROUND Recent studies suggest that rare codon clusters are functionally important for protein activity. METHODS Here, for the first time we analyzed and reported rare codon clusters in Hepatitis C Virus (HCV) genome and then identified the location of these rare codon clusters in the structure of HCV protein. This analysis was performed using the Sherlocc program that detects statistically ...

Beta thalassemia is the  most common autosomal recessive disorder. The present study reports a rare β globin gene mutation, HBB: c.180G>A: codon 59 (AAG/AAA), in a patient from Gilan province, northern Iran. Nucleotide sequencing of amplified DNA belonging to a 35 years old man presenting mild hypochromia revealed a synonymous mutation due to a G>A conversion at the third position of codon 59 o...

beta thalassemia is the  most common autosomal recessive disorder. the present study reports a rare β globin gene mutation, hbb: c.180g>a: codon 59 (aag/aaa), in a patient from gilan province, northern iran. nucleotide sequencing of amplified dna belonging to a 35 years old man presenting mild hypochromia revealed a synonymous mutation due to a g>a conversion at the third position of codon 59 o...

Synonymous rare codons are considered to be sub-optimal for gene expression because they are translated more slowly than common codons. Yet surprisingly, many protein coding sequences include large clusters of synonymous rare codons. Rare codons at the 5' terminus of coding sequences have been shown to increase translational efficiency. Although a general functional role for synonymous rare cod...

Most amino acids are encoded by more than one codon. These synonymous codons are not used with equal frequency: in every organism, some codons are used more commonly, while others are more rare. Though the encoded protein sequence is identical, selective pressures favor more common codons for enhanced translation speed and fidelity. However, rare codons persist, presumably due to neutral drift....

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...

Background: Cholestatic disorders are divided in the extra and intra-hepatic that created due to the severe liver diseases. ABCB11 encodes the bile salt export pump and this gene is mutated in several forms of intrahepatic cholestasis. So far, some molecular features of this gene was studies.Objective: Using a developed web server, we identified high number of rare codons in this gene, and four...

MOTIVATION An increasing amount of evidence from experimental and computational analysis suggests that rare codon clusters are functionally important for protein activity. Most of the studies on rare codon clusters were performed on a limited number of proteins or protein families. In the present study, we present the Sherlocc program and how it can be used for large scale protein family analys...