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Motif Finding

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Question 2: Motif finding
Try a number of motif-finding algorithms covered in the lab, and try different parameters. What
good motif can you find from the sequence? Here are some useful hints for the analysis (depends
on the software you are using):
? Motif width ~ 13, and search in both strands of the DNA
? Ask each algorithm to report the best 3-10 motifs
? Each sequence contains 0-n copies of the motif
? If possible, specify the background as yeast (or S. cerevisiae) intergenic or yeast genome
? If the same motif was reported by different algorithms, it is likely real and good

a) What is the motif consensus (most frequent nucleotide at each position)?

b) Select the single motif you like best, cut the motif hit sites, and generate the MotifLogo from
http://weblogo.berkeley.edu/logo.cgi.

c) Write a document with brief description of what motif tools you used, a quick summary of what you got, and a picture of the SequenceLogo. Please be brief here (less than 2 pages total).

Please see attached python file and perform the analysis.

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About question 2, they are gene names in the data2 text file. in addition to the questions in Q2, please write:

A document with brief description of what motif tools you used, a quick
summary of what you got, and a picture of the SequenceLogo. Please be brief.

Attached is the notes on the motifs.

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