Answer the following questions regarding Computing the Dot Plot. Please answer a

Question

Answer the following questions regarding Computing the Dot Plot. Please answer all parts

Eile Edit Yew Hbtory Bookmarks bols Help e SakaieURI: csc ospri.. X lab10-bioinfo lab10-bioi.. X C Chegg Study I Guided Sol X Search https sakai. uriedu/access/lessonbuilder/item/11693426/group/e3dbb580-16f5-490f-aff0-88196032a87 /Lab 10 Bioinformatics Algorithms 4-10 Mab10-bioin A Most visited e Getting started Let's now practice the technique to compute a dot plot with sliding windows. We will use a small example to demonstrate how this will work: 0 A 2 G 3 T 4 A If we assume a window size of 3 and a threshold of 0.5, then we put a dot in the dot plot in position (0,0) if we have better than a 50% match between the first three characters in the first sequence and the first three characters in the second sequence. In this example, we would be comparing: AGG AAG

Explanation / Answer

string1:-AGGTAAG

string2:-AAGTA

Cell(0,2):- we are comparing strings GTA and AAG. Nothing match so no dot is placed

Cell(0,3):- we are comparing strings TAA and AAG. One letter matches which is 33.3% and below the threshold so no dot is placed.

Cell(0,4):- we are comparing strings AAG and AAG. Complete match so we put a dot.

Cell(0,5):- we dont have enough characters so we append a symbol $ to the string which is not relevant to any string. So we are comparing strings AG$ and AAG. One letter matches which is 33.3% and below the threshold so no dot is placed.

Cell(0,6):- again we dont have enough characters so we append a symbol $ to the string which is not relevant to any string. So we are comparing strings G$$ and AAG. Nothing match so no dot is placed

When filling in cells (0,5) and (0,6) the problem we encountered is string length is less than 3 so we appended a character which is not relevant to both strings and wont give wrong results while calculating.

For cells of the form (1,x) the second string to be taken is AGT

Similarly for cells of the form (2,x) the second string to be taken is GTA, for (3,x) it is TA$, for (4,x) it is A$$

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