Sequence alignment is the procedure of comparing two (pair-wise alignment) or more multiple sequences by searching for a series of individual characters or patterns that are in the same order in the sequences.
• Pair-wise alignment: compare two sequences
• Multiple sequence alignment: compare more than two sequences
Pairwise alignment can be either global or local
In global alignment, an attempt is made to align the entire sequence.
• If two sequences have approximately the same length and are quite similar, they are suitable for the global alignment.
• Suitable for aligning two closely related sequences
Local alignment concentrates on finding stretches of sequences with high level of matches
• Finds local regions with the highest level of similarity between the two sequences and aligns these regions without considering the alignment of rest of the sequence regions
• Suitable for aligning more divergent sequences
• Used for finding out conserved patterns in DNA or protein sequences
What is the purpose of sequence alignment?
By finding similarities between sequences
1. Scientists can infer the function of newly sequenced genes by aligning the newly sequenced genes with sequences already in the database
2. Predict new members of gene families
3. Discovering evolutionary relationships or reconstruction of phylogeny
-To find whether two (or more) genes or proteins are evolutionarily related to each other in closely related species
4. It can be used to predict the location and function of protein-coding and transcription-regulation regions in genomic DNA. Regulatory regions in genome are often conserved therefore presence of such conserved regions easily tells us the regulatory sites in the newly sequenced genes
5. To find structurally or functionally similar regions within proteins