Select best protein codeing genes from models Generated from MAKER2, Cufflinks and any de novo assembling programs. Previously we published a paper describing how it works. In that paper, we call it MCOT.
Cao, X.; Jiang, H. Integrated Modeling of Protein-Coding Genes in the Manduca Sexta Genome Using RNA-Seq Data from the Biochemical Model Insect. Insect Biochemistry and Molecular Biology 2015, 62, 210. http://www.sciencedirect.com/science/article/pii/S0965174815000144
Download version 1.0 described in the paper from this link. https://github.com/ATPs/MCuNovo/releases/tag/v1.0
version 2.0 is not ready yet. I am trying to update the program so that it is easier to use. It will work on Linux
This name is from MAKER, Cufflinks and de novo.
Cao X., Jiang H. (2019) Integrated Modeling of Structural Genes Using MCuNovo. In: Brown S., Pfrender M. (eds) Insect Genomics. Methods in Molecular Biology, vol 1858. Humana Press, New York, NY https://link.springer.com/protocol/10.1007%2F978-1-4939-8775-7_5
Leave any comments here in github. If you are interested in using MCuNovo, I will be glad to provide help. If you have any thoughts or special needs, I would like to provide solutions if possible.
MCuNovo is developed for Manduca sexta genome project. It also works for species with similar sequencing data. I've already improved some parts, like use Muscle instead of blastp to do protein sequence comparisons, but I haven't include that in the main program. I can improve the program, if there is such need.
Best. :)