| Chapter title |
A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes
|
|---|---|
| Chapter number | 7 |
| Book title |
Comparative Genomics
|
| Published in |
Methods in molecular biology, January 2018
|
| DOI | 10.1007/978-1-4939-7463-4_7 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-7461-0, 978-1-4939-7463-4
|
| Authors |
Danillo Oliveira Alvarenga, Leandro M. Moreira, Mick Chandler, Alessandro M. Varani, Oliveira Alvarenga, Danillo, Moreira, Leandro M., Chandler, Mick, Varani, Alessandro M. |
| Abstract |
Mobile genetic elements (MGEs) are an important feature of prokaryote genomes but are seldom well annotated and, consequently, are often underestimated. MGEs include transposons (Tn), insertion sequences (ISs), prophages, genomic islands (GEIs), integrons, and integrative and conjugative elements (ICEs). They are intimately involved in genome evolution and promote phenomena such as genomic expansion and rearrangement, emergence of virulence and pathogenicity, and symbiosis. In spite of the annotation bottleneck, there are so far at least 75 different programs and databases dedicated to prokaryotic MGE analysis and annotation, and this number is rapidly growing. Here, we present a practical guide to explore, compare, and visualize prokaryote MGEs using a combination of available software and databases tailored to small scale genome analyses. This protocol can be coupled with expert MGE annotation and exploited for evolutionary and comparative genomic analyses. |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Canada | 1 | 17% |
| Unknown | 5 | 83% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 3 | 50% |
| Members of the public | 3 | 50% |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 51 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 13 | 25% |
| Student > Master | 6 | 12% |
| Student > Doctoral Student | 5 | 10% |
| Student > Bachelor | 5 | 10% |
| Researcher | 5 | 10% |
| Other | 3 | 6% |
| Unknown | 14 | 27% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 13 | 25% |
| Biochemistry, Genetics and Molecular Biology | 7 | 14% |
| Immunology and Microbiology | 6 | 12% |
| Environmental Science | 2 | 4% |
| Veterinary Science and Veterinary Medicine | 2 | 4% |
| Other | 7 | 14% |
| Unknown | 14 | 27% |