Lecture_3_motifs

markov cluster algorithm finds a natural grouping of

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Unformatted text preview: no efficient exact solutions 42 7 9/2/13 Mo,fs: Profiles and Consensus a C a a C Alignment G c c c c g A g g g t t t t t a a T C a c c A c c T g g A g t t t t G 3 1 0 1 1 4 0 0 1 0 3 1 0 0 1 4 _________________ Profile A C G T 3 2 0 0 0 4 1 0 1 0 4 0 0 0 0 5 _________________ Consensus ACGTACGT •  Line up the pa]erns by their start indexes s = (s1, s2, …, st) •  Construct matrix profile with frequencies of each nucleo,de in columns •  Consensus nucleo,de in each posi,on has the highest score in column Biological Interpreta,on of the Consensus •  Think of consensus as an “ancestor” mo,f, from which mutated mo,fs emerged. •  The distance between a real mo,f and the consensus sequence is generally less than that for two real mo,fs. Defining Some Terms A Visualiza,on of Mo,f Parameters n DNA L d si s=(s1, s2,… st) number of sample DNA sequences sample of DNA sequences length of the mo,f (L- mer) Maximum distance star,ng posi,on of an L- mer in sequence i array of mo,f’s star,ng posi,ons DNA L=8 cctgatagacgctatctggctatccaGgtacTtaggtcctctgtgcgaatctatgcgtttccaaccat agtactggtgtacatttgatCcAtacgtacaccggcaacctgaaacaaacgctcagaaccagaagtgc n=5 aaacgtTAgtgcaccctctttcttcgtggctctggccaacgagggctgatgtataagacgaaaatttt agcctccgatgtaagtcatagctgtaactattacctgccacccctattacatcttacgtCcAtataca ctgttatacaacgcgtcatggcggggtatgcgttttggtcgtcgtacgctcgatcgttaCcgtacgGc n = 69 s= s1 = 26...
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This note was uploaded on 02/10/2014 for the course CS 425 taught by Professor Asaben-hur during the Fall '13 term at Colorado State.

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