PySSRstat
PySSRstat is a set of Python command-line programs that extract further statistical data about microsatellites or simple sequence repeats (SSR) from the output of the MISA program (Thiel et al, 2003).
The additional data comprise:
- relative abundance
- relative density
- longest motifs by repeat length
- total abundance of repeat types in absolute numbers and percentage
Furthermore, the microsatellites found by MISA can be filtered for minimum and maximum repeat length and subsequently for the presence of a border for later primer selection.
PySSRstat was written for and used in Galasso and Ponzoni (2015).
The programs of PySSRstat are written by Mario Nenno in the Python 3.4 language and tested on a PC with Core i5-4570, 8 GB RAM under MS Windows 8.1
All programs of PySSRstat are copyright 2015 by Mario Nenno and distributed under the terms of the Revised BSD License.
Download PySSRstat from Github
References
- Galasso, I. and Ponzoni, E. (2015)
- In Silico Exploration of Cannabis sativa L. Genome for Simple Sequence Repeats (SSRs). American Journal of Plant Sciences, 6, 3244-3250. doi: 10.4236/ajps.2015.619315
- Thiel T., Michalek W., Varshney R., Graner A. (2003)
- Exploiting EST databases for the development and characterization of
gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied
Genetics 106: 411-422.
Link: http://pgrc.ipk-gatersleben.de/misa/