Kindly help me to find software which can digest the cattle whole genome in silico so that i can use it for ddRAD sequencing
Hello Vineeth,
The full version of Geneious can perform in silico digestion with a relatively large number of predefined restriciton enzymes. However, the license is a little costly.
If you have a little programming experience, you can perform the same task using a relatively simple script. There are already some python scripts out there looking for trypsin dirgestion, which you can easily modify.
Good Luck
There are several available. I wrote one for a class project (https://github.com/tkchafin/fragmatic) in Perl. Here is another as an R package, if you prefer working in R: https://cran.r-project.org/web/packages/SimRAD/SimRAD.pdf.
Thank you Tyler Chafin and Claudia Pätzold for your valuable suggestions.
Try Unipro Ugene, it is a free software with almost all the functions similar to a highly priced commercial software.
Okonechnikov K, Golosova O, Fursov M, the UGENE team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012 28: 1166-1167. doi:10.1093/bioinformatics/bts091
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