NDLI: Analysis of synonymous codon usage in the Cas1 gene of Riemerella anatipestifer

Content Provider	IEEE Xplore Digital Library
Author	Yang He Anchun Cheng Mingshu Wang
Copyright Year	2012
Description	Author affiliation: Inst. of Preventive Veterinary Med., Sichuan Agric. Univ., Chengdu, China (Yang He; Anchun Cheng; Mingshu Wang)
Abstract	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 content at the 3rd codon position (GC3s), and the codon adaptation index (CAI) was computed with the help of CHIPS, CUSP, and CAI programs of EMBOSS. Result: The results suggested that Cas1 genes in RA and its 11 reference strains applied the relatively similar pattern of codon usage with similar sequence length, CAI, and ENc values, and all of them were lowly expressed genes. The codon bias pattern of Cas1 genes in RA and its reference strains was closely related to their gene function. The plots of ENc versus GC3s indicated that the genetic heterogeneity of these genes observed herein was constrained by GC composition. Besides, RA Cas1 gene preferred A or/and T ending codons to G or/and C ending codons, and the bias corresponded to high A+T content in RA cas1 gene. GC compositional constraint was found to be a major determinant of codon usage in RA Cas1 gene. Additionally, The comparison of the codon preference of RA Cas1 gene with those of E. coli, yeast, and human, revealed that codon usage varied among different organisms and the codon usage pattern of RA Cas1 gene was similar to that of yeast. Accordingly, it can be speculated that yeast was a well suited host for heterologous expression of RA Cas1 gene. Conclusion: Bioinformatics analysis plays an important role in research of genes. And using bioinformatics method, the paper provides a foundational understanding of the molecular evolution and function of RA Cas1 gene, as well as contributes significantly to guiding the further study of the gene.
Starting Page	1138
Ending Page	1146
File Size	333286
Page Count	9
File Format	PDF
ISBN	9781467311830
e-ISBN	9781467311847
DOI	10.1109/BMEI.2012.6512980
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-16
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Cas1 gene Riemerella anatipestifer bioinformatics codon usage
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Similar Documents

Analysis of synonymous codon usage in the mfs_1 gene of Riemerella anatipestifer

Analysis of synonymous codon usage in the outer membrane efflux protein gene of Riemerella anatipestifer

Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

Bioinformatics analysis of the complete nucleotide sequence of the Riemerella anatipestifer D15 gene

Bioinformatics analysis of surface antigen D15 protein encoded by the D15 gene of Riemerella anatipestifer

Analysis of synonymous codon usage in the UL41 gene of duck plague virus

Characterization for mfs_1 gene from Riemerella anatipestifer by bioinformatics analysis

Bioinformatic characterization of epsA Gene from Riemerella anatipestifer

Sequence analysis of the OmpA/MotB gene from Riemerella anatipestifer by bioinformatics

Analysis of synonymous codon usage in the Cas1 gene of Riemerella anatipestifer