Genomic Databases

A topical collection in Genes (ISSN 2073-4425).

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Editor

Department of Biosciences, University of Milan (UNIMI), 20122 Milano MI, Italy
Interests: plant genomics; evolutionary genomics; polyploidy; bioinformatics; databases; sequence assembly; solanacea; domestication
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

The development of next-generation sequencing (NGS) at the beginning of 21st century has produced an incredible amount of sequencing data. The data have been used in a wide range of scientific studies, from the development of reference genomes to expression profiling of thousands of genes. Due to the data volume as well as the complexity of the data, they need special platforms in order to be efficiently managed and made accessible to the community.

There are different types of platforms, from gigantic genomic data repositories with little data curation such as GenBank, ENA or the Genome Sequence Archive to project-specific genomic databases with variable levels of data curation. The levels of data curation are one of the determining factors not only in the usability of these platforms, but also in how they meet the needs of the specific communities that they target. Most of these databases have associated popular tools with graphical interfaces, such as BLAST, Gbrowser and JBrowser. Others may have developed their specific set of tools to present data specifically linked to a project.

The goal of this collection is to present to the scientific community some genomic databases that have been developed in recent years.

In order to maximize the usability of the publications associated with the databases, we propose a “concept paper” format.

Dr. Aureliano Bombarely
Guest Editor

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Keywords

  • genomics
  • databases
  • data curation
  • genomic data analysis

Published Papers (1 paper)

2020

8 pages, 2952 KiB  
Article
DetR DB: A Database of Ionizing Radiation Resistance Determinants
by Alina Ryabova, Olga Kozlova, Azat Kadirov, Anastasiia Ananeva, Oleg Gusev and Elena Shagimardanova
Genes 2020, 11(12), 1477; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11121477 - 09 Dec 2020
Cited by 3 | Viewed by 2592
Abstract
Nuclear pollution is an urgent environmental issue and is a consequence of rapid industrialization and nuclear accidents in the past. Remediation of nuclear polluted sites using microbial vital activity (bioremediation) is a promising approach to recover contaminated areas in an environmentally friendly and [...] Read more.
Nuclear pollution is an urgent environmental issue and is a consequence of rapid industrialization and nuclear accidents in the past. Remediation of nuclear polluted sites using microbial vital activity (bioremediation) is a promising approach to recover contaminated areas in an environmentally friendly and cost-saving way. At the same time, the number of known bacterial and archaeal species able to withstand extremely high doses of ionizing radiation (IR) is steadily growing every year, together with growing knowledge about mechanisms of radioresistance that opens up opportunities for developing new biotechnological solutions. However, these data are often not systemized, and can be difficult to access. Here, we present the Determinants of Radioresistance Database, or DetR DB, gathering a comprehensive catalog of radioresistant microbes and their molecular and genetic determinants of enhanced IR tolerance. The database provides search tools, including taxonomy, common gene name, and BLAST. DetR DB will be a useful tool for the research community by facilitating the extraction of the necessary information to help further analysis of radiation-resistant mechanisms. Full article
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