Sequence Alignment

A sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. The number of identical and similar amino acid residues may be compared to the total number of amino acids in the protein. This gives the percentage of identical and similar residues-percentage of sequence identity and sequence similarity. Similar residues are those that have similar chemical characteristics. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. The important models for sequence analysis are GLOBAL ALIGNMENT, LOCAL ALIGNMENT and GAP PENALTY. The Smith waterman algorithm is a local alignment algorithm which is able to identify mutation in DNA sequences. The various methods for sequence alignment include BRUTE FORCE, DOT MATRIX, DYNAMIC PROGRAMMING, HEURISTICS METHODS. Scoring matrices are used for computing alignment scores, based on observed substitution rates derived from the substitution frequencies. The most popular two scoring matrices are PAM and BLOSUM matrices.