IMPORTANCE AND

SIGNIFICANCE OF
SEQUENCE ALIGNMENT
• Sequence alignment arranges two or more nucleotide or amino acid
sequences to identify regions of similarity between the sequences.
These regions of similarity are helpful in understanding the functional,
structural, and evolutionary relationships between the sequences.
• Two commonly used sequence alignment algorithms are global
alignment and local alignment.
• Sequence alignment arranges two or more nucleotide or amino acid
sequences to identify regions of similarity between the sequences.
These regions of similarity are helpful in understanding the functional,
structural, and evolutionary relationships between the sequences.
• Two commonly used sequence alignment algorithms are global
alignment and local alignment.
• Global alignment: Global alignment is a method of comparing two
sequences, which aligns the entire length of the sequences by
maximizing the overall similarity. This method is used when
comparing sequences that are of the same length.
• Local alignment: In local alignment, instead of attempting to align the
entire length of the sequences, only the regions with the highest
density of matches are aligned. This is useful for identifying short
conserved regions in protein or nucleotide sequences.
• Types of Sequence Alignment
• A. Pairwise Alignment
• Pairwise sequence alignment is the type of sequence
alignment that involves aligning two sequences to identify
the optimal pairing of the sequences.
• It is based on a scoring system that assigns positive scores
to matching characters and negative scores to mismatching
characters or gaps.
• The main objective of pairwise sequence alignment is to
obtain the highest possible score, which indicates the
degree of similarity between the two sequences.
• B. Multiple Sequence Alignment
• Multiple Sequence Alignment involves aligning multiple
(three or more) biological sequences to achieve optimal
sequence matching.
• Multiple sequence alignments are used to identify
conserved sequence regions and to construct
phylogenetic trees, which help us understand the
functional and evolutionary relationships between
different species or groups of organisms.
• Methods of pairwise sequence alignment
• There are three main methods for generating pairwise alignments:
• A. Dot-matrix method
• Dot matrix method, also known as the dot plot method, is a graphical
method of sequence alignment that involves comparing two
sequences by plotting them in a two-dimensional matrix.
• In a dot matrix, two sequences that must be compared are plotted
along a matrix’s horizontal and vertical axes. The method then scans
each residue of one sequence to identify similarities with all residues
in the other sequence.
• If a residue in one sequence matches a residue in the other sequence, a
dot is placed in the corresponding position in the matrix. Otherwise, the
matrix position is left blank.
• If the two sequences being compared are highly similar, the dot plot will
display as a single line along the matrix’s main diagonal. However, when
the sequences are less similar, the dot plot will show more scattered
dots with fewer diagonal lines, indicating that the sequences share less
similarity.
• Dot plots can also find repeat elements in a single sequence. Short
parallel lines above and below the main diagonal indicate the presence
of repeats.
• Dot plots can also find repeat elements in a single sequence. Short
parallel lines above and below the main diagonal indicate the
presence of repeats.
• B. Dynamic programming
• Dynamic programming is used to find the optimal alignment between
two proteins or nucleic acid sequences by comparing all possible pairs
of characters in the sequences.
• Dynamic programming can be used to produce both global and local
alignments. The global pairwise alignment algorithm using dynamic
programming is based on the Needleman-Wunsch algorithm, while
the dynamic programming in local alignment is based on the Smith-
Waterman algorithm.
• This method works in the following three steps.
• Initialization of the scoring matrix: The first step is to create a two-
dimensional matrix where the two sequences to be aligned are
written along the top and left sides. The matrix is initialized with gap
penalties and an initial score of zero at the top-left corner.
• Matrix filling with maximum scores: The next step involves filling the
matrix with scores based on a scoring matrix. Scoring matrices for
nucleotide sequences are simple. A positive value is given for a match,
and a negative value for a mismatch. For amino acids, BLOSUM and
PAM scoring matrices are used.
• To calculate the alignment scores, the algorithm starts at the upper
left corner of the matrix and proceeds one row at a time toward the
lower right corner. The algorithm fills each cell in the matrix with the
maximum score that can be obtained by aligning the corresponding
residues.
• Traceback to identify optimal alignment: After filling the matrix, the
algorithm performs a traceback to find the optimal alignment path.
Starting from the bottom-right corner and moving towards the top-
left corner, adjacent cells are examined in reverse order to determine
the best path with the highest total score. The optimal alignment path
is the one with the maximum score.
• C. Word or k-tuple method
• Word or k-tuple methods are heuristic methods best known for their
use in the database search tools FASTA and BLAST.
• The word method is a fast method for aligning two sequences. It
begins by identifying short identical sequences, also known as words
or k-tuples, and then uses dynamic programming to align the
sequences based on these words.