In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence alignment, searches against biological databases, and others.

Since the development of methods of high-throughput production of gene and protein sequences, the rate of addition of new sequences to the databases increased very rapidly. Such a collection of sequences does not, by itself, increase the scientist's understanding of the biology of organisms. However, comparing these new sequences to those with known functions is a key way of understanding the biology of an organism from which the new sequence comes. Thus, sequence analysis can be used to assign function to genes and proteins by the study of the similarities between the compared sequences. Nowadays, there are many tools and techniques that provide the sequence comparisons (sequence alignment) and analyze the alignment product to understand its biology.

Sequence analysis in molecular biology includes a very wide range of relevant topics:

1. The comparison of sequences in order to find similarity, often to infer if they are related (homologous)
2. Identification of intrinsic features of the sequence such as active sites, post translational modification sites, gene-structures, reading frames, distributions of introns and exons and regulatory elements
3. Identification of sequence differences and variations such as point mutations and single nucleotide polymorphism (SNP) in order to get the genetic marker.
4. Revealing the evolution and genetic diversity of sequences and organisms
5. Identification of molecular structure from sequence alone

In chemistry, sequence analysis comprises techniques used to determine the sequence of a polymer formed of several monomers (see Sequence analysis of synthetic polymers). In molecular biology and genetics, the same process is called simply "sequencing".

In marketing, sequence analysis is often used in analytical customer relationship management applications, such as NPTB models (Next Product to Buy).

In social sciences and in sociology in particular, sequence methods are increasingly used to study life-course and career trajectories, time use, patterns of organizational and national development, conversation and interaction structure, and the problem of work/family synchrony. This body of research is described under sequence analysis in social sciences.