The term sequence analysis in biology implies subjecting a DNA or peptide sequence to sequence alignment, sequence databases, repeated sequence searches, or other bioinformatics methods on a computer.

Sequence analysis in molecular biology and bioinformatics is an automated, computer-based examination of characteristical fragments, e.g. of a DNA-strand. It basically includes five biologically relevant topics:

1. the comparison of sequences in order to find similar sequences (sequence alignment)
2. identification of gene-structures, reading frames, distributions of introns and exons and regulatory elements
3. prediction of protein structures
4. genome mapping
5. comparison of homologous sequences to construct a molecular phylogeny