bioin.replication.pattern_matching¶

bioin.replication.pattern_matching(pattern, genome)[source]¶

Find all occurrences of a pattern in a string.

Parameters:	pattern (str) – pattern string to search in the genome string. genome (str) – search space for pattern.
Returns:	List, list of int, i.e. all starting positions in genome where pattern appears as a substring.

Examples

Find all the starting positions for a pattern string in the genome string.

>>> pattern = 'ATAT'
>>> genome = 'GATATATGCATATACTT'
>>> positions = pattern_matching(pattern, genome)
>>> positions
    [1, 3, 9]

>>> pattern = 'CTTGATCAT'
>>> genome = 'CTTGATCATCTTGATCATCTTGATCAT'
>>> positions = pattern_matching(pattern, genome)
>>> positions
    [0, 9, 18]