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BI379_F09_Exercise_2_key - TGTTTA MA0040(or FoxQ1 Visually...

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BI379 F09 Exercise 2 Key B: Do and write out answers to Math Minute 2.2 Discovery Questions 1-4. 1. Explain how the sequence logo represents the information in table MM2.1 – The position weight table shows numerical representations of the likelyhood of any given nucleotide at a particular position in the sequence. The sequence logo graphically represents this by stacking the Base letters (color coded) on top of one another. The height of the letter indicates two things. First of all, the relative heights (with respect to one another) tell you which is the most common nucleotide. Second, the combined height tells you how “important” the position is. For example, if only one nucleotide is seen 80% of the time and another 20%, the sequence at that position is extremely important (and the stack is high). If all four nucleotides are seen equally often, the sequence at that position is unimportant (and the stack is low). 2. Which of these transcription factors is most likely to bind to DNA containing the motif
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Unformatted text preview: TGTTTA? MA0040 (or FoxQ1). Visually, this sequence logo matches the motif best. To assess it quantitatively, we could plug in the motif and position weight matrix into the pwm.xls form. 3. atatatataggctgg – 10.95 ctatatatatgctgg – 10.55 ctataaataggccgg – 14.99 – best TATA box 4. The sequence shown is the reverse complement of the best match in Q3. Therefore, the TATA box is on the other strand (and the gene points the other way). C: Do and write out answers to Discovery Questions 2-12 and 2-13. Q 2-12 – Testcode values 1: 0.549 2: 0.468 3: 0.961 – best value The third sequence has the ORF. Q 2-13 -- Scrambling obviously randomizes the amino acid sequence, leaving it unlikely that a large ORF could be formed. This part of the exercise is merely meant to illustrate that the discovery of a good ORF most likely indicates a real gene as opposed to just a chance arrangement of amino acids with no stop codon....
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