Pairwise Sequence Comparison

The major advantage of the dot matrix method for finding sequence alignments is that all possible matches of residues between two sequences are found, leaving the investigator the choice of identifying the most significant ones. Then, sequences of the actual regions that align can be detected by using one of two other methods for performing sequence alignments, e.g., dynamic programming. These methods are automatic and usually show one best or optimal alignment, even though there may be several different, nearly alike alignments. Alignments generated by these programs can be compared to the dot matrix alignment to determine whether the longest regions are being matched and whether insertions and deletions are located in the most reasonable places.

In the dot matrix method of sequence comparison, one sequence (A) is listed across the top of a page and the other sequence (B) is listed down the left side, as illustrated in Figures 3.4 and 3.5. Starting with the first character in B, one then moves across the page keeping in the first row and placing a dot in any column where the character in A is the same. The second character in B is then compared to the entire A sequence, and a dot is placed in row 2 wherever a match occurs. This process is continued until the page is filled with dots representing all the possible matches of A characters with B characters. Any region of similar sequence is revealed by a diagonal row of dots. Isolated dots not on the diagonal represent random matches that are probably not related to any significant alignment.

Detection of matching regions may be improved by filtering out random matches in a dot matrix. Filtering is achieved by using a sliding window to compare the two sequences. Instead of comparing single sequence positions, a window of adjacent positions in the two

Dot Matrix Dna

Figure 3.4. Dot matrix analysis of DNA sequences encoding phage X cI (vertical sequence) and phage P22 c2 (horizontal sequence) repressors. This analysis was performed using the dot matrix display of the Macintosh DNA sequence analysis program DNA Strider, vers. 1.3. The window size was 11 and the stringency 7, meaning that a dot is printed at a matrix position only if 7 out of the next 11 positions in the sequences are identical.

Figure 3.4. Dot matrix analysis of DNA sequences encoding phage X cI (vertical sequence) and phage P22 c2 (horizontal sequence) repressors. This analysis was performed using the dot matrix display of the Macintosh DNA sequence analysis program DNA Strider, vers. 1.3. The window size was 11 and the stringency 7, meaning that a dot is printed at a matrix position only if 7 out of the next 11 positions in the sequences are identical.

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