A Tool for Multiple Targeted Genome Deletions that Is Precise, Scar-Free, and Suitable for Automation.

Autor: Wayne Aubrey, Michael C Riley, Michael Young, Ross D King, Stephen G Oliver, Amanda Clare

Publikováno v: PLoS ONE, Vol 10, Iss 12, p e0142494 (2015)

Many advances in synthetic biology require the removal of a large number of genomic elements from a genome. Most existing deletion methods leave behind markers, and as there are a limited number of markers, such methods can only be applied a fixed nu

Externí odkaz: https://doaj.org/article/b196bc3d488b4aa2b0de9e7f4a44686b

PD5: a general purpose library for primer design software.

Autor: Michael C Riley, Wayne Aubrey, Michael Young, Amanda Clare

Publikováno v: PLoS ONE, Vol 8, Iss 11, p e80156 (2013)

Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this

Externí odkaz: https://doaj.org/article/da55dc78fdc148b2a6b4f5179964ebb2

Automated pseudogene detection reveals insights into historical gene sharing dynamics in prokaryotes

Autor: Nicholas J Dimonaco, Wayne Aubrey, Amanda Clare, Kim Kenobi, Chris Creevey

Publikováno v: Access Microbiology. 4

In recent years it has become apparent that prokaryotic genomes contain large numbers of pseudogenised genes which may provide valuable insights into the recent functional history of an organism. However, pseudogenes are difficult to detectab initioa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::edb185be3fae935b118bc40bbb4a61e3
https://doi.org/10.1099/acmi.ac2021.po0147

No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study

Autor: Kim Kenobi, Wayne Aubrey, Nicholas Dimonaco, Amanda Clare, Chris Creevey

Publikováno v: Dimonaco, N J, Aubrey, W, Kenobi, K, Clare, A & Creevey, C J 2022, ' No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study ', Bioinformatics, vol. 38, no. 5, pp. 1198-1207 . https://doi.org/10.1093/bioinformatics/btab827

Motivation The biases in CoDing Sequence (CDS) prediction tools, which have been based on historic genomic annotations from model organisms, impact our understanding of novel genomes and metagenomes. This hinders the discovery of new genomic informat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bd49eb4695cb9fd7cd07be9623b8f5de
https://pure.qub.ac.uk/en/publications/83701cf9-769f-4028-bca4-d7ba91cc28b3

On the complexity of haplotyping a microbial community

Autor: Amanda Clare, Samuel M. Nicholls, Leander Schietgat, Kurt De Grave, Christopher J. Creevey, Wayne Aubrey

Publikováno v: Nicholls, S M, Aubrey, W, De Grave, K, Schietgat, L, Creevey, C J & Clare, A 2021, ' On the complexity of haplotyping a microbial community ', Bioinformatics, vol. 37, no. 10, pp. 1360-1366 . https://doi.org/10.1093/bioinformatics/btaa977
Bioinformatics

Motivation Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolating and sequ

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0ae842035e25e13795b8e8af5a653dbf
https://pure.qub.ac.uk/en/publications/on-the-complexity-of-haplotyping-a-microbial-community(06bfd352-688c-47d2-9e0e-3aaa0d6160af).html