In this chapter, you will learn how to align sequences using freely available software on the WWW and from private servers. I will refer to nucleotides throughout this chapter, but you could just as easily align two protein sequences.
Sequence alignment is a useful tool with many, diverse applications.
You might want to compare a new sequence against an established sequence that you have fetched from a molecular database, for example. On the other hand, you might be sequencing a new gene, in which case it is imperative that you sequence it accurately. Sequence alignment involves metaphorically placing one sequence above the other and comparing the aligned vertical pairs at each position. Two nucleotide or protein sequences can be compared against each other, quickly and accurately, by using computer software. Nucleotide sequences could be aligned manually, but automation speeds up the laborious process and eliminates the risk of human error.