SEQUENCE ALIGNMENT AND PHYLOGENY

Sequence alignment is the technique used to find and compare pairs of related sequences. Multiple sequence alignment is the alignment of three or more sequences with gaps inserted in the sequences such that residues with common structural positions and/ or ancestral residues are aligned in the same column.

Alignment is the most basic component of biological sequence manipulation, and it has diverse applications in sequence annotation, structural and functional predictions for genes and proteins, phyiogeny and evolutionary analysis. The basic information multiple sequence alignment can provide is identification of conserved sequence regions. This is very useful in designing experiments to test and modify the function of specific proteins, in predicting the function and structure of proteins, and in identifying new members of protein families.

Four basic steps are involved in multiple sequence alignment

1. Selecting DNA or protein sequences,
2. Inputting into an automatic multiple sequence alignment Program such as ClustalX,
3. Editing alignments, and
4. Interpreting the alignments.