Question

Name your file “DMx1_Your last name_Your first name.”

You can use MS Word to complete the matrices (go to Insert, Table, Insert table, fill the table). Save the file as a PDF file.

If you draw the matrices on paper, take pictures. Make sure the pictures are clear and readable.

Insert the pictures in MS Word document and save it as a PDF file.

1. Align using dot matrix:

horizontal sequence – AGGCTCCC, vertical sequence – GCGCTCCG.

Trace and explain the features below the matrix.

2. Do the noise reduction in the previous matrix using three sets of rules.

  A. Window size 2 x 2, mm limit = 0, dot position (1, 1)

  B. Window size 3 x 3, mm limit = 1, dot position (3, 3)

  C. Window size 3 x 3, mm limit = 0, dot position (2, 2)

For each set of rules, use a separate matrix.

Answer 1

1. Here the solution for compare to sequence using dot matrix or diagram method and here the two sequences, so some principle applies here at the horizontal sequence – AGGCTCCC, vertical sequence – GCGCTCCG, we need to make row and column which same as punnett square, this is small representation what's going on big scale.

we have to compare the sequence which matches from the top & left hand side. the black dot denotes the matching sequences. if you observe above diagram, you will see G to G, C to C, T to T and so on. when you observe above the diagram, now need to connect the dots and we can do many different computation for example in ideal situations, we would have 8 coincidences of same letters but here we have 6 that means we have 6 out 8 coincidences. of the letters on both strands, whic is 6/8.

2 A. Window size 2 X 2, mm limit = 0, dot position(1,1), the dot matrix diagram will be:

the table represent 2 X 2 in which the position sequence GC to GC.

B & C: The table represents 3 X 3 sequence representation:

In the dot matrix, two sequences to be compared are written in the horizontal and vertical axes of matrix. to reduce the noise, instead using a single residue to scan similarity, a filtering technique, has to be applied, which uses window of fixed length converting a stretch of residue pairs. when applying filtering, windows side across the two sequences to compare all possible stretches. Dots are only placed when a stretch residues equal to window size from one sequence matches completely with a stretch of another sequence. the window is also called a tuple, the size of which can be manipulated so that clear pattern of sequence match can be plotted. however, if the selected window size is too long, sensitivity alignment is lost.