Computational protocol: Particle Swarm Optimization with Reinforcement Learning for the Prediction of CpG Islands in the Human Genome

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Protocol publication

[…] In PSO, four different parameters need to be set: the population size, the number of iterations, and the C1 and C2 constants of the update function. The population size in our study was set to 300 , the number of iterations was set to 100, and C1 and C2 were set to 2 . The CpGIS parameters were: length set to 200 bp, GC content set to 50%, O/E ratio set to 0.6, and the gap between adjacent islands set to 100 bp (http://cpgislands.usc.edu/). CpGcluster parameters used were: p-value threshold of 1E-5 and distance threshold (percentile) of 50. CpGProd and CpGplot were used directly from the internet (http://pbil.univ-lyon1.fr/software/cpgprod_query.html and http://www.ebi.ac.uk/Tools/emboss/cpgplot/index.html). […]

Pipeline specifications

Software tools CpGcluster, CpGProD, EMBOSS
Application Genome annotation
Organisms Homo sapiens