Pairwise sequence alignment is the alignment of sequences. Pairwise alignment does not mean the alignment of two sequences it may be more than between two sequences. It gives the higher similarity regions and least regions of differences.
For example, there are two sequences:
Sequence A: CGGATCAT
Sequence B: CTTAACT
An alignment of A and B:
CGGATCA – T sequence A
C – – – TTAACT sequence B
There are three types of pairwise sequence alignment
 Dot matrix analysis
 Dynamic Programming
 Word or Ktuple method
Dot Matrix Analysis
 This method clearly shows the similarities between the two closely relates sequences
 There are two sequences A and B.The sequence A is written on the top of the matrix and sequence B written vertically on the left side of the matrix
 Now starting from sequence B see the character in the sequence A where the character of match A and B match put the dot there.
 Continue to put the dots according to matches.
 These dots give us a diagonal row of dots
 The dots rather than diagonal shows the random matches
Dot Matrix Comparison
This matrix tells us about the similarities between the two closely related sequence.This diagonal shows the similarities between these sequences
Similarities mean no of characters(nucleotide) matches in both sequences. similarities show the relationship between organisms and their ancestors. It shows how much they are the same in their function and structure.
 It shows the insertion or deletion that tells us about mutations. If there is a mutation in sequence the diagonal will shift. It is not possible to tell whether the shifted diagonal is due to insertion or deletion so we call it “indels”.
 It also tell us about “palindromic sequences”.
Palindromic sequences mean the sequences that remain same if we read it from left to right or right to left. If there are some perpendicular diagonal at the original diagonal it will show the palindromic sequences.
 It also predicts gene duplications. Gene duplication gives the parallel diagonal in the matrix.
Advantages and Disadvantages of Dot Matrix
Pairwise Sequence Alignment Advantages
The position of dots tell us about the region of alignment.it gives all possible alignment or diagonals. Human brain and eyes are used in this method
Disadvantages of Pairwise Sequence Alignment
The major disadvantage of this method is that it does not give us optimal alignment.
Dynamic Programming Method
To get the optimal alignment we use dynamic programming method. It tells us about gaps that could be a mutation. These gaps can represent by “—“.
We use two methods in the dynamic programming method.

Local Alignment

Global Alignment
In local alignment, we use Smithwatermann method while in global alignment Needlemanwunch method is used. There is a little bit difference between these two methods. In needlemannwunsch algorithm, there are three values as one value of diagonal, second for match or miss match and the third one is of gap penalty. While in smithwatermann algorithm we use four values instead of three. The fourth value that we use is zero. The advantage of this zero is that we replace this zero with any negative number in the matrix. In SW algorithm we move to top left from the maximum value present anywhere in the matrix.
The word or Ktuple Method
It is the heuristic method, give not optimal alignment but better than the dynamic programming. Actually, the dynamic programming method could not be used for large databases that’s why we prefer the Ktuple method when we search a single query along with a huge database or alignment.
K tuple means a string of k words. For example for nucleotide K=11 and for protein K=3.
K method is implemented in the FASTA and BLAST family. In FASTA to search a database, the specific length of words=k is defined by the user. It is not so fast but it is susceptible at a low value of k. In BLAST algorithms are used for specific queries and matches distantly related sequence.