This module wraps the code referred to by the following article for use in the RAST and BV-BRC genome annotation services:
Identification, variation and transcription of pneumococcal repeat sequences. Croucher NJ1, Vernikos GS, Parkhill J, Bentley SD. BMC Genomics. 2011 Feb 18;12:120. doi: 10.1186/1471-2164-12-120.
The underlying code and databases are available at ftp://ftp.sanger.ac.uk/pub/pathogens/strep_repeats/.
From the paper:
Small interspersed repeats are commonly found in many bacterial chromosomes. Two families of repeats (BOX and RUP) have previously been identified in the genome of Streptococcus pneumoniae, a nasopharyngeal commensal and respiratory pathogen of humans. However, little is known about the role they play in pneumococcal genetics.
This module is a component of the BV-BRC build system. It is designed to fit into the
dev_container infrastructure which manages development and production deployment of
the components of the BV-BRC. More documentation is available here.