Shrikant Pawar, Department of Computer Science, Georgia State University, 34 Peachtree Street, 30303, Atlanta, GA, USA.
Aditya Stanam, College of Public Health, The University of Iowa, UI Research Park, #219 IREH, 52242-5000, Iowa City, Iowa, USA.
Ying Zhu Creative Media Industries Institute and Department of Computer Science, Georgia State University, 34 Peachtree Street, 30303, Atlanta, GA, USA.
Journal of Bioinformatics and Sequence Analysis, Journal Year: 2018, Volume and Issue: Vol.9(2), P. 10 - 14

Published: July 31, 2018

Bioinformatics is an emerging field, where information technology usage can significantly accelerate life science research. It is a relatively new field and the scope of exploring new tools and techniques seems immense. One major field where bioinformatics plays important role is next generation sequence analysis (NGS), in which an unknown genome is shuttered into pieces and tried to align it to a reference known genome to decipher its functions using sequence comparison. The first well known application of this technology is the human genome project which took nearly 10 years to finish. With advancements in central processing units (CPUs), the …

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Takaaki Kamatani, Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Kitasenzoku 2-1-1, Ota City, Tokyo, 145-8515, Japan.
Tatsuo Shirota Department of Oral and Maxillofacial Surgery, Showa University School of Dentistry, Kitasenzoku 2-1-1, Ota City, Tokyo, 145-8515, Japan.
Journal of Bioinformatics and Sequence Analysis, Journal Year: 2018, Volume and Issue: Vol.9(1), P. 1 - 9

Published: Jan. 31, 2018

Indices of codon usage pattern of human papillomavirus (HPV) were analyzed to understand the key determinants of synonymous codon usage in the HPV genome. The complete sequences of 39 HPV genomes were downloaded from the website of the National Center for Biotechnology Information. The relative synonymous codon usage values, effective number of codons, GC content, percentage of GCs at the third position of synonymous codons (GC3s), codon adaptation index, hydrophobicity, aromaticity of conceptually translated gene products were calculated using the Codon W 1.4.2 program. HPV preferentially used codons ending with A/U. By comparing relative synonymous codon usage of the HPV …

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