Difference between revisions of "MarkerMiner"
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Revision as of 21:21, 6 December 2019
Description
MarkerMiner compares user-provided transcriptomic data input against reference databases of known single-copy nuclear genes that were identified as part of a systematic survey of duplication-resistant genes in 17 angiosperm genomes by De Smet et al. (2013). The reference databases are composed of Orthologous Groups (OGs) that were constructed using data from the PLAZA 2.5 database (Van Bel et al. 2011) and the OrthoMCL method (Li et al. 2003).
DeSmet et al. (2013) classified OGs as single-copy if they were present across all 17 genomes. However, missing copies in up to two species or duplicates in up to three species were tolerated to accommodate possible variations in the reference genome annotations and the presence of recent duplicates or pseudogenes, respectively. Single-copy genes were classified as "Strictly" single-copy if OGs were truly single-copy for all species or "Mostly" single-copy if the OGs were duplicated in at least one or to up to three other surveyed species.
Required Modules
Serial
- markerminer
System Variables
- HPC_MARKERMINER_DIR - installation directory
Validation
- Validate 4/5/2018