TriNecklace

A necklace algorithm to determine the growth function of trinucleotide circular codes

About

Supporting software for the paper A necklace algorithm to determine the growth function of trinucleotide circular codes, openly published and available here: http://www.scienpress.com/journal_focus.asp?Main_Id=57&Sub_id=IV&Issue=859. When refering to this software, please cite

@Article{HMZ13,
 author = {Herrmann, M. and Michel, C. and Zugmeyer, B.},
 title = {A necklace algorithm to determine the growth function of trinucleotide circular codes},
 journal = {Journal of Applied Mathematics and Bioinformatics},
 volume = {3},
 pages = {1-40},
 year = {2013},
}

How to use

This is an eclipse project. Import the project and launch gui.Main. You will be presented with a GUI with several parameters:

• Lenght: count the number of trinucleotide circular codes for that length
• Maximal: only count maximal code
• Threads: number of threads to launch
• Partition number: number of jobs shared among all threads (they pick one job at a time)
• Output file: save the results in a file