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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/
www.nenno.it by Mario Nenno, © 2007 All rights reserved. 12/18/2018 19:10