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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.

Since the development of methods of high-throughput production of gene and protein sequences during the 90s, the rate of addition of new sequences to the databases increases continuously. Such a collection of sequences does not, by itself, increase the scientist's understanding of the biology of organisms. However, comparing sequences with known functions with these new sequences is one way of understanding the biology of that 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 the biology.

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

1. The comparison of sequences in order to find similarity and dissimilarity in compared sequences (sequence alignment)
2. Identification of gene-structures, reading frames, distributions of introns and exons and regulatory elements
3. Finding and comparing point mutations or the single nucleotide polymorphism (SNP) in organism in order to get the genetic marker.
4. Revealing the evolution and genetic diversity of organisms.
5. Function annotation of genes.

In chemistry, sequence analysis comprises techniques used to do determine the sequence of a polymer formed of several monomers. 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).

Methodology

For sequence alignment method compose of pairwise alignment (align with two sequences) and multiple alignment (align with more than two sequence). There are several tools for alignment, including: ClustalW, PROBCONS, MUSCLE, MAFFT, DIALIGN, T-Coffee, POA, and MANGO.

There are many algorithms used in the study of sequence analysis. These include: dynamic programming, Hidden Markov Model, Viterbi and Greedy.