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The codon usage bias of DPV UL19 gene and 25 reference herpesviruses have been analyzed in this study. This work was performed by program CodonW 1.4, and CUSP and CHIPS of EMBOSS. The results indicated that codons of DPV UL19 gene were strong bias towards the synonymous codons with A or T at the third codon position. The codon adaptation index (CAI), effective number of codons (ENC), and GC3s values...
The aim was to identify the codon usage bias between the newly identified Riemerella Anatipestifer(RA)outer membrane efflux protein gene(GenBank accession NO. CP003388) and outer membrane efflux protein genes of 17 other reference flavobacteriaceae with bioinformatics software. A comparative analysis of the codon usage bias of the 18 flavobacteriaceae was performed by using the CodonW1.4.2 and CUSP...
Object: The study herein was aimed to provide a comprehensive analysis of synonymous codon usage in Riemerella anatipestifer (RA) Cas1 gene and a comparative study of the codon usage bias between RA and other 11 reference strains within the Flavobacteriaceae family. Methods: Using bioinformatics method, the values of relative synonymous codon usage (RSCU), the effective number of codons (ENc), G+C...
In order to have some bioinformatics information about synonymous codon usage pattern of the duck enteritis virus (DEV) US10 gene (GenBank accession number: EU195084), we analyzed the DEV US10 gene and 19 other reference herpesviruses by using bioinformatics softwares, such as CAI, CHIPS and CUSP program of EMBOSS. The results revealed that codon usage bias in the US10 gene was mainly influenced by...
The bioinformatics analysis of D15 gene, encoding the 99-kDa major surface antigen D15 of Riemerella anatipestifer, the etiological agent of septicemia anserum exsudativa, was first provided in this article. The program DNAStar, ORF Finder, CDD, ClustalX, MEGA, NetNGlyc, NetOGlyc as well as NetPhos were performed to predict the characteristic of the D15 gene in physicochemical, construction of phylogenetic...
The OmpA/MotB gene from Riemerella anatipestifer (RA) by our lab was sequenced. And the molecular characteristic of this gene was analyzed by computational gene and protein in bioinformatics. The result indicated that an open reading frame(ORF) containing 379bp nucleotides was preliminarily identified by aligning with gene bank database by software of BlastN and ORF Finder. The relative molecular...
The bioinformatics analysis of mfs_1 gene from Riemerella anatipestifer (RA) by kinds of bioinformatics software, such as BLASTN2.2.14, ORF Finder, BLASTP and FASTA procedures, DNAstar 7.0, Chips and Cusp programs of the EMBOSS, SignalP V4.0 Server, ProtScale, BepiPred1.0 Server, PredictProtein Sever, PSORT and MEGA software. Importing the sequence into all of these bioinformatics software in the...
The synonymous codon usage in the UL41 gene of duck plague virus (DPV) and 21 reference herpesviruses have been investigated by using the CodonW 1.4 program, CUSP (create a codon usage table) program and CHIPS(calculated ENC value) of EMBOSS (The European Molecular Biology Open Software Suite). The results reveals that the synonymous codons with A and T at the third codon positon have widely usage...
In the past years, a number of conventional and advanced bioinformatics methods have been employed for predicting gene structure and function. Here, we used many bioinformatics softwares to analyse the duck plague virus US10 gene (GenBank accession number: EU195084). The results indicated that this gene encoded an estimated 322 putative protein, contained the conserved domain of the Gene66 (IR5) protein...
The analysis on codon usage bias of major facilitator superfamily mfs_1 gene of Riemerella anatipestifer (RA) may improve our understanding of the evolution and pathogenesis of RA and provide a basis for understanding the relevant mechanism for biased usage of synonymous codons and for selecting appropriate expression systems to improve the expression of target genes. All of these analysis results...
Duck plague virus (DPV) is a widespread virus in all members of the family Anatidae of the order Anseriformes, and it has been classified into the family Herpesviridae. In this study, the relative synonymous codon usage (RSCU) values, effective number of codons (ENC) values, and the frequencies of nucleotide G + C at the third position (GC3s) contents were investigated, meanwhile, a comparative analysis...
D15 protein which encoded by the RA-D15 gene was one of the Riemerella anatipestifer's surface antigens. The precursor RA-D15 protein was encoded by 859 amino acid residues, which was 99-kDa in theoretical molecular weight. The putative protein had no signal peptide, 32 potential antigenic determinants. RA-D15 protein was a type membrane protein that could be divided into 3 distinct functional domains:...
This report showed some physico-chemical properties and structural features about UL41 protein predicted by some software and on-line tools. The analysis showed both the signal peptide and the trans membrance region are not found. Meanwhile, the protein has twenty-four potential phosphorylation sites. In addition, the protein has more hydrophilic amine acid districts than hydrophobic districts and...
The Duck Plague Virus (DPV) is the causative agent of Duck plague, which causes significant economic losses in the commercial duck industry all over the world. Our laboratory had identified and sequenced the DPV UL41 gene. Bioinformatics analysis of DPV UL41 gene were performed by some software and online tools. The results showed that GC content of duck plague virus UL41 gene was 42.42%, which encoded...
In the study, we calculated the codon usage bias in the newly identified UL38 gene of Duck Enteritis Virus (DEV) and performed a correlation analysis of codon bias of DEV UL38 gene and its host animal. There was a strong bias in the DEV UL38 gene towards the synonymous codons with A and T at the third codon position. The amino acids codon usage bias in the DEV UL38 gene was compared with other 15...
Glycoprotein K encoded by the DEV-UL53 gene is one of the DEV envelope glycoproteins. Like most members of the alphaherpesvirinae, the genes in the UL region of its genome are well conserved, which means that the major DEV envelope glycoprotein K possessing similar functions of envelope glycoprotein K of alphaherpesvirinae plays an essential role in viral replication and cell fusion. Glycoprotein...
Prediction of B cell epitopes of duck enteritis virus (DEV) VP19c protein encoded by UL38 gene and expression in prokaryotic system were described in the present study. The major antigenic portion of VP19c protein of DEV was predicted and corresponding gene was amplified from the extracted DNA and cloned. The recombinant expression construction(pPAL7-truncated UL38) was identified by the polymerase...
In order to understand the relevant mechanism for biased usage of synonymous codons and the evolution and pathogenesis of DEV better, as well as for selecting appropriate expression systems to improve the expression of the target genes, we performed a comparative analysis of the codon usage bias in the UL47 gene of the duck enteritis virus (DEV) and the 26 reference herpesviruses. The results indicated...
The glycoprotein I (gI) gene homologue of duck plague virus (DPV) was cloned by degenerate polymerase chain reaction (PCR) and sequenced. DPV gI gene open reading frame (ORF) was 1116 bp in length and its primary translation product was a polypeptide of 371 amino acids long. Comparison with other herpesvirus revealed higher similarity, had a close evolution relationship with members of the genus Mardivirus...
The analysis on codon usage bias of Us4 gene of Duck Plague Virus (DPV) may provide a basis for understanding the evolution and pathogenesis of DPV and for selecting appropriate host expression systems to improve the expression of target genes in vivo and in vitro. In this study, the synonymous codon usage in the Us4 gene of DPV and 17 reference herpesviruses have been investigated . The results reveals...
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