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Mobile genetic elements: the agents of open source evolution
TLDR
This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics. Expand
Diversity of bacterial type II toxin–antitoxin systems: a comprehensive search and functional analysis of novel families
TLDR
It is proposed that due to their addictive properties, TA systems are likely to be maintained in chromosomes even though they do not necessarily confer an advantage to their bacterial hosts. Expand
Prophinder: a computational tool for prophage prediction in prokaryotic genomes
TLDR
UNLABELLED Prophinder is a prophage prediction tool coupled with a prediction database, a web server and web service that will enable further studies of prophages contribution to the bacteriophage gene pool and to better understand gene shuffling between prophaging and phages infecting the same host. Expand
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
TLDR
The current status of docking procedures for predicting protein–protein interactions starting from their three‐dimensional structure is assessed from a first major evaluation of blind predictions, which reveals genuine progress but also illustrates the remaining serious limitations and points out the need for better scoring functions and more effective ways for handling conformational flexibility. Expand
Reticulate representation of evolutionary and functional relationships between phage genomes.
TLDR
2 classification schemes are proposed that provide an automatic and dynamic way of representing the relationships within the phage population and can be extended to include newly sequenced phage genomes, as well as other types of genetic elements. Expand
ACLAME: A CLAssification of Mobile genetic Elements
TLDR
The ACLAME database is a collection and classification of prokaryotic mobile genetic elements from various sources, comprising all known phage genomes, plasmids and transposons, and aims to build a comprehensive classification of the functional modules of MGEs at the protein, gene and higher levels. Expand
ACLAME: A CLAssification of Mobile genetic Elements, update 2010
TLDR
The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids), and numerous tools for in-depth analysis of the results have been added. Expand
Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
TLDR
Results and a brief survey of the methods used by participants of CAPRI Rounds 3–5 suggest that genuine progress in the performance of docking methods is being achieved, with CAPRI acting as the catalyst. Expand
Evidence for copper homeostasis function of metallothionein (MT3) in the hyperaccumulator Thlaspi caerulescens
TLDR
Functional testing in yeast and Northern blot analysis added further evidence for adaptative variations of MT3 for the maintenance of Cu homeostasis in a metal hyperaccumulator. Expand
Variations in plant metallothioneins: the heavy metal hyperaccumulator Thlaspi caerulescens as a study case
TLDR
Thlaspi caerulescens is a model Zn/Cd hyperaccumulator and thus constitutes an ideal system to study the variability of plant metallothioneins, and functional complementation in yeast was used to assess whether these variations may alter the MTs’ function in T. caerULescens. Expand
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