Sequence Alignment

Abstract

Sequence alignment involves establishing correspondences between bases or codons of DNA or RNA strings or between amino acids forming linear sequences in proteins. Aligning DNA, RNA or amino acid sequences is of basic importance in genomics, proteomics and transcriptomics and can be used for a variety of research purposes. It can find similarity between two DNA sequences resulting from the existence of a recent common ancestor, which these two sequences originate from. By measuring or computing distances between the aligned sequences, one draw inferences about the evolutionary processes they have gone through. This inference about the evolutionary process may involve estimating the time that has passed from the common ancestor to the present, but may also involve stating hypotheses or reconstructing a single evolutionary event in the past or a sequence of them. Aligning two sequences can allow one to detect their overlap or to notice that one sequence is a part of the other or that the two sequences share a subsequence. Instead of two sequences, one can also align many sequences or match a sequence against a DNA, RNA, or protein database. Multiple alignments of RNA or amino acid sequences in proteins allow one to infer their secondary and tertiary structures as well as active or functionally important sites in proteins.