Good Morning Magdalena: Please note this source directory:
http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=tree;f=src/utils/cpgIslandExt Note the README information about the evolution of this source. --Hiram Magdalena Potok wrote: > To whom it may concern: > > I am interested in obtaining the program that was used in generating the CpG > Islands for the zebrafish genome found on UCSC genome browser, or more > information pertaining to the first section of identifying maximally coring > segment. Is this program publically available or could I get in touch with > the person who ran this program? > > Thank You, > > Magdalena Potok ( graduate student in Brad Cairns Lab at the University of > Utah). > > > Below is the description form UCSC on the CpG island track: > > CpG islands were predicted by searching the sequence one base at a time, > scoring each dinucleotide (+17 for CG and -1 for others) and identifying > maximally scoring segments. Each segment was then evaluated for the following > criteria: > > * GC content of 50% or greater > * length greater than 200 bp > * ratio greater than 0.6 of observed number of CG dinucleotides to the > expected number on the basis of the number of Gs and Cs in the segment > The CpG count is the number of CG dinucleotides in the island. The Percentage > CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. > The ratio of observed to expected CpG is calculated according to the formula > (cited in Gardiner-Garden et al. (1987)): > Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G) > where N = length of sequence. > > Credits > This track was generated using a modification of a program developed by G. > Miklem and L. Hillier (unpublished). _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
