bioin.motif.randomized_motif_search¶

bioin.motif.randomized_motif_search(dna, k, t)[source]¶

Return a list of best k-mers from each of t different strings dna. Compare score_pseudo of the k-mer.

Parameters:	dna (list) – matrix, has t rows. k (int) – k-mer. t (integer) – t is the number of k-mers in dna to return, also equal to the row number of dna 2D matrix.
Returns:	List, a list of t k-mers strings, each k-mer from each of t different strings dna.

Examples

RandomMotifs(Dna, k, t) that uses random.randint to choose a random k-mer from each of t different strings Dna, and returns a list of t strings.

>>> dna = ['CGCCCCTCTCGGGGGTGTTCAGTAAACGGCCA', 'GGGCGAGGTATGTGTAAGTGCCAAGGTGCCAG', 'TAGTACCGAGACCGAAAGAAGTATACAGGCGT', 'TAGATCAAGTTTCAGGTGCACGTCGGTGAACC', 'AATCCACCAGCTCCACGTGCAATGTTGGCCTA']
>>> k = 8
>>> t = 5
>>> random_best_t_kmers = randomized_motif_search(dna, k, t)
>>> random_best_t_kmers
    ['CGGGGGTG', 'TGTAAGTG', 'TACAGGCG', 'TTCAGGTG', 'TCCACGTG']