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...

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 Hepatitis B virus (HBV) as an infectious disease that has nine genotypes (A - I) and a 'putative' genotype J. OBJECTIVES The aim of this study was to identify the rare codon clusters (RCC) in the HBV genome and to evaluate these RCCs in the HBV proteins structure. METHODS For detection of protein family accession numbers (Pfam) in HBV proteins, the UniProt database and Pfam searc...

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 ...

to be sure, that a program behaves correctly at runtime; the behavior of the program should be verified. where the program source code is available, it is possible to extract the operational logic (i.e., behavior) of the program. but in this paper, programs are considered as black boxes, so no information is available about the operational logic of programs. however, some efforts are spent to l...