alignment

[Alignment]

In bioinformatics, alignment refers to a mapping betweenequivalentamino acids (in the case of proteins) or nuceotides (in the case of DNA or RNA). In the case of proteins, we usually consider two basic types of alignment, sequence alignment and structure alignment. In sequence alignment, only the amino acid sequences are compared; in structure alignment, the 3D coordinates are compared. There are hybrid methods which include both types of information as well as methods that use other types of information such as secondary structure, solvent exposure, etc..