What is TYPSimSelector?
The TYPSimSelector sorts identity by state (IBS) values derived from SNP datasets using PLINK v1.07 for accessions in the Ames Diversity Panel (Romay et al., 2013; submitted).
The tool available here was conceived and implemented originally by Mark Millard at the North Central Regional Plant Introduction Station (NCRPIS) to enable the use of genomic similarity for germplasm management.
Recognizing that this sort of analysis would be useful for others as well, a collaboration to deploy the mechanism via MaizeGDB was initiated in 2013.
This tool was developed by Emily Mauch with guidance from Carson Andorf, Mark Millard, Cinta Romay, Ed Buckler, Candy Gardner, and Carolyn Lawrence.
As described by Romay et al. the Ames Diversity Panel is a
set of approximately 2,500 maize accessions primarily made available via the NCRPIS in Ames, IA.
The panel was interrogated using over 680,000 SNP markers to establish identity by state (IBS) relationships.
This has proven useful for examining relationships between lines based upon similarity and divergence scores
(where identical lines are assigned a similarity score of 1 and a divergence is measured as 1-similarity).
How Similarity Scores were Calculated
Similarity scores were calculated as described by Romay, MC et al. 2013
Identity by state (IBS) was calculated for all possible pairwise
comparisons using PLINK v1.07 (Purcell et al., 2007).
Cite This Tool
If you are using the TYPSimSelector for your research then please cite MaizeGDB and Romay et. al. as follows:
Andorf CM, Cannon EK, Portwood JL, Gardiner JM, Harper LC, Schaeffer ML, Braun BL, Campbell DA, Vinnakota AG, Sribalusu VV, Huerta M, Cho KT, Wimalanathan K, Richter JD, Mauch ED, Rao BS, Birkett SM, Sen TZ, Lawrence-Dill CJ. MaizeGDB update: new tools, data and interface for the maize model organism database. Nucleic Acids Res. 2016 Jan 4;44(D1):D1195-201. doi: 10.1093/nar/gkv1007. Epub 2015 Oct 1.
|Romay et. al.:
Romay, MC et al. 2013. Genome Biology 14:R55