| Chapter title |
Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs
|
|---|---|
| Chapter number | 15 |
| Book title |
Viral Metagenomics
|
| Published in |
Methods in molecular biology, January 2018
|
| DOI | 10.1007/978-1-4939-7683-6_15 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-7682-9, 978-1-4939-7683-6
|
| Authors |
Aysan Ghasemzadeh, Marta Małgorzata ter Haar, Masoud Shams-bakhsh, Walter Pirovano, Vitantonio Pantaleo |
| Abstract |
Next-generation sequencing has opened the door to the reconstruction of viral populations and examination of the composition of mutant spectra in infected cells, tissues, and host organisms. In this chapter we present details on the use of the Shannon entropy method to estimate the site-specific nucleotide relative variability of turnip crinkle virus, a positive (+) stranded RNA plant virus, in a large dataset of short RNAs of Cicer arietinum L., a natural reservoir of the virus. We propose this method as a viral metagenomics tool to provide a more detailed description of the viral quasispecies in infected plant tissue. Viral replicative fitness relates to an optimal composition of variants that provide the molecular basis of virus behavior in the complex environment of natural infections. A complete description of viral quasispecies may have implications in determining fitness landscapes for host-virus coexistence and help to design specific diagnostic protocols and antiviral strategies. |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Netherlands | 4 | 36% |
| India | 1 | 9% |
| Mexico | 1 | 9% |
| Unknown | 5 | 45% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 6 | 55% |
| Members of the public | 5 | 45% |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 13 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 5 | 38% |
| Student > Ph. D. Student | 3 | 23% |
| Professor > Associate Professor | 2 | 15% |
| Professor | 1 | 8% |
| Unspecified | 1 | 8% |
| Other | 0 | 0% |
| Unknown | 1 | 8% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 5 | 38% |
| Biochemistry, Genetics and Molecular Biology | 2 | 15% |
| Environmental Science | 1 | 8% |
| Veterinary Science and Veterinary Medicine | 1 | 8% |
| Unspecified | 1 | 8% |
| Other | 1 | 8% |
| Unknown | 2 | 15% |