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- person_outline Robert Schmitz
Publication for FASTmC
Epigenomic diversification within the genus Lupinus
[…] DNA was isolated from leaf tissue and MethylC-seq libraries were prepared for each species as was previously described [, ]. As no sequenced and assembled genome exists for Lupinus spp., we used FASTmC, which is a non-reference-based approach to estimate the levels of DNA methylation in the CG, CHG (H = A|C|T) and CHH sequence contexts . Briefly, linear models were created for each sequence […]
Evolution of DNA Methylation across Insects
[…] ast squares (PGLS) was used to correlate continuously categorized estimates of DNA methylation generated through WGBS and alignment to reference assemblies (methylpy), or nonreferenced based methods (FASTmC) to discretely coded social traits (eusocial, subsocial, communal, and solitary). BEAST 2 () was used to estimate a multilocus coalescent tree, which was used to control for relatedness of spec […]
A Comparative Analysis of 5 Azacytidine and Zebularine Induced DNA Demethylation
[…] oncentration and methylation loss was less highly correlated (AZA r2= 0.65; ZEB r2 = 0.61). A second replicate of seedlings treated with 100 µM AZA and ZEB using low coverage sequencing combined with FASTmC analysis confirmed the genome-wide loss of DNA methylation (see Materials and Methods) (Table S3). Although this technique is less sensitive, it also shows a concentration-dependent decrease in […]
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