PhasomeIt – identification and classification of SSR-mediated PV loci

PhasomeIt is a software tool for identifying and grouping phase variable loci in a group of genomes. It identifies PV loci based on the presence of short simple sequence repeats (SSRs) (found using Bossref) and then uses BLAST to group the loci present in all genomes into homology groups. It will then output this data into HTML format (see here for an example output for Campylobacter). PhasomeIt is written in Python (version 3.3.5 or above) but requires Bossref to function and the BLAST+ suite installed to run from the default path. The BioPython and NatSort python packages are also required.

PhasomeIt can be downloaded from here (version 1.1.1, earlier versions are available on request).

Bossref for Windows and Linux is included in the download, but requires a 64-bit Intel-compatible processor. Note that when running on Linux you may need to set the executable permission bit on the ‘bossref’ file included in the download for it to function.

Citation

Publication is currently in preparation.

PSAnalyse – rapid analysis tool for use with GeneScan

PSAnalyse is a software tool for the length and state analysis of phase variable loci. It is described at length in the publication given below, and the latest version can be downloaded from here. The PSAnalyse.pl script contained in the .zip is written in Perl 5 and portable to any system running this software. The PSAnalyse.exe file is a packaged version of this script for use on Windows systems without Perl installed. PSAanalyse_PC.exe is a C# frontend for this script allowing use of the program without resorting to the command line

Citation

Lango-Scholey, L.; Aidley, J.; Woodacre, A.; Jones, M. A; Bayliss, C. D. (2016) High Throughput Method for Analysis of Repeat Number for 28 Phase Variable Loci of Campylobacter jejuni Strain NCTC11168, PLoS ONE 11(7): e0159634 (doi:10.1371/journal.pone.0159634)

Bossref – high speed identification of tandem repeat sequences

Bossref is a tool for high speed identification of perfect Tandem Repeat Sequences in genome data. It uses the XOR boolean operator and it’s name is derived from BOolean Simple Sequence REpeat Finder. It is available for use under the MIT license, meaning you can use the software for any purpose of your choosing

At the present time, only a 64-bit version of Bossref is available. It can be downloaded for Windows or for Linux (Intel x86-64 only). These executable files carry no warranty of any kind, and you should treat them with the same caution you treat any executable downloaded from the internet.

Source code will be made available upon publication.

Citation

Publication is currently in preparation.