The program is intended to search for CpG islands in sequences.
Program options:
Min length of island to find - searching CpG islands with a length (bp) not less than specified in the field.
Min percent G and C - searching CpG islands with a composition not less than specified in the field.
Min CpG number - the minimal number of CpG dinucleotides in the island.
Min gc_ratio=P(CpG)/(expected)P(CpG) - the minimal ratio of the observed to expected frequency of CpG dinucleotide in the island.
Extend island if its lengths less then required - extending the CpG island, if its length is shorter than required.
Output example:
Search parameters: len: 200 %GC: 50.0 CpG number: 0 P(CpG)/exp: 0.600 extend island: no A: 21 B: -2 Locus name: 9003..16734 note="CpG_island (%GC=65.4, o/e=0.70, #CpGs=577)" Locus reference: expected P(CpG): 0.086 length: 25020 20.1%(a) 29.9%(c) 28.6%(g) 21.4%(t) 0.0%(other) FOUND 4 ISLANDS # start end chain CpG %CG CG/GC P(CpG)/exp P(CpG) len 1 9192 10496 + 161 73.0 0.847 0.927( 1.44) 0.123 1305 2 11147 11939 + 87 69.2 0.821 0.917( 1.28) 0.110 793 3 15957 16374 + 57 79.4 0.781 0.871( 1.60) 0.137 418 4 14689 15091 + 49 74.2 0.817 0.887( 1.42) 0.122 403