Sequence Alignment

Sequence alignment is the way of comparing two (pair-wise) or more (multiple) primary sequences of DNA/RNA or protein to identify regions of similarity (i.e., searching for a series of individual characters or character patterns that are in the same order in the sequences), that maybe a consequence of functional, structural, or evolutionary relationships between the sequences.
Two sequences are aligned by writing them across a page in two rows. Identical or similar characters are placed in the same column. And non-identical characters are places in the same column as a mismatch or opposite a gap in the sequence.
In an optimal alignment, non-identical characters and gaps are placed to bring as many identical or similar characters as possible.

"-" represents a gap
"*" represents a match
":" represents a mismatch

If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. In protein sequence alignment, the degree of similarity between amino acids occupying a particular position in the sequence can be interpreted as a rough measure of how conserved a particular region or sequence motif is among lineages. The absence of substitutions, or the presence of only very conservative substitutions in a particular region of the sequence, suggest that this region has structural or functional importance. Although DNA and RNA nucleotide bases are more similar to each other than to amino acids, the conservation of base pairing can indicate a similar functional or structural role.

TYPES OF SEQUENCE ALIGNMENT

1) Pairwise Sequence Alignment.
2) Multiple Sequence Alignment.

Sequence Alignment and Sequence Comparison is more or less the same. Only after the sequences are aligned, they can be compared.