An alignment refers to the procedure of comparing two or more sequences by looking for a series of individual characters or character patterns that are in the same order in the sequences. Identical or similar characters are placed in the same column, and non- identical characters can either be placed in the same column as a mismatch or opposite to a gap in one of the other sequences. In an optimal alignment, non-identical characters and gaps are so placed to bring as many identical or similar characters as possible into vertical register. Two types of sequence alignment have been recognized, Global and local. The global alignment optimizes the alignment over the full-length of the sequences. In local alignment, stretches of sequence with the highest density of matches are given the highest priority. The following is an example of global and local alignment.
Global alignment:
LGPSTKDFGKISESREFDN
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LNQLERSFGKINMRLEDA
The alignment is stretched over the entire sequence lengths to include as many matching amino acids as possible up to and including the sequence ends. Although there is an obvious region of identity in this example ( the sequence FGKI), a global alignment may not align such regions in order to favor matching more amino acids along the entire sequence length.
Local alignment:
----------FGKI----------
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----------FGKI----------
Local alignment of the same sequences as above. In this case, the alignment tends to stop at the ends of regions of identity or strong similarity. A much higher priority is given to finding these local regions than to extending the alignment to include more neighboring amino acid pairs. Dashes indicate sequence not included in the alignment. This type of alignment favors finding conserved amino acid motifs in related protein sequences.