Biology subjects

Torsten Seemann

Publications and source records attributed to Torsten Seemann.

3 recordsLinked to original sources

bioRxiv2016

Refutation: Spontaneous secondary mutations confound analysis of the essential two component system WalKR in Staphylococcus aureus

Ji et al.,1 recently detailed the structure of the extracytoplasmic Per-Arnt-Sim (PAS) domain of WalK (WalKEC-PAS), the sensor kinase of the essential two-component system WalKR in Staphylococcus aureus. The authors made two independent walK mutants in S. aureus, each with a single amino acid alteration in WalKEC-PAS. They postulated from comparative structural analysis and primary sequence comparisons that these residues might be important for extra cellular signal transduction. We have also been exploring the function of WalKR and were surprised by the striking phenotypic impact of a single amino acid substitutions in the WalK sensor, which were contrary to our own unpublished observations.\n\nThe authors subjected their WalKEC-PAS mutants (WalKD119A and WalKVl49A) to a series of phenotypic screens to probe the function of this domain. Compared to the parental methicillin sensiti ...

Microbiology↗

bioRxiv2016

NGMASTER: in silico Multi-Antigen Sequence Typing for Neisseria gonorrhoeae

Whole-genome sequencing (WGS) provides the highest resolution analysis for comparison of bacterial isolates in public health microbiology. However, although increasingly being used routinely for some pathogens such as Listeria monocytogenes and Salmonella enterica, the use of WGS is still limited for other organisms, such as Neisseria gonorrhoeae. Multi-antigen sequence typing (NG-MAST) is the most widely performed typing method for epidemiologic surveillance of gonorrhoea. Here, we present NGMASTER - a command-line software tool for performing in silico NG-MAST on assembled genome data. NGMASTER rapidly and accurately determined the NG-MAST of 630 assembled genomes, facilitating comparisons between WGS and previously published gonorrhoea epidemiological studies. The source code and user documentation are available at https://github.com/MDU-PHL/ngmaster.

Genomics↗

bioRxiv2016

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.

Bioinformatics↗