Biology subjects

Paul P Gardner

Publications and source records attributed to Paul P Gardner.

3 recordsLinked to original sources

bioRxiv2016

Comparative distribution of antisense-RNA regulated toxin-antitoxin systems

Toxin-antitoxin (TA) systems are gene modules that appear to be widely horizontally mobile. It has been proposed that type I TA systems, with an antisense RNA-antitoxin, are less mobile than other TAs but no direct comparisons have been made. We searched for type I, II and III toxin families on chromosomes, plasmids and phages across bacterial phyla.The distribution of type I TA systems were more narrow than most type II and III system families, though this was less true of more recently discovered families.We discuss how the function and phenotypes of type I TA systems as well as biases in our databases and discovery of these modules may account for differences in their distribution.

Bioinformatics↗

bioRxiv2015

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

MotivationNext generation sequencing technologies have provided us with a wealth of information on genetic variation, but predicting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics.\n\nResultsWe present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms.\n\nAvailabilityA program implementing DBS for pairwise genome comparisons is freely available at: https://github.com/UCanCompBio/deltaBS.\n\nContactnicole.wheeler@pg.canterbury.ac.nz, lars.barquist@uni-wuerzburg.de\n\nSupplementary informationSupplementary data are available at BioRxiv online.

Bioinformatics↗

bioRxiv2014

Annotating RNA motifs in sequences and alignments

RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterise RNA motifs, which are the central building blocks of RNA structure. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterised RNAs. Moreover, we introduce a new profile-based database of RNA motifs - RMfam - and illustrate its application for investigating the evolution and functional characterisation of RNA.\n\nAll the data and scripts associated with this work is available from: https://github.com/ppgardne/RMfam

Bioinformatics↗