Sequence Alignment and Homology Search

UMMS Affiliation

Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology

Publication Date


Document Type



Bioinformatics | Computational Biology | Genomics


Bioinformatics was brought into the spotlight in the late 1990s through the Human Genome Project. With the rapid accumulation of completed genomes, it was soon realized that for the vast majority of the newly identified genes and other functional regions of the genomes there were no other biological data. One way of inferring biological function is through homology: Because homologous genes have a common evolutionary descent, they are likely to have the same biological function. A large number of bioinformatics tools have been designed for rapidly and accurately comparing sequences of genes or proteins, comparing gene sequences with genomes, and comparing genomes. Two widely used tools for sequence alignment and homology searches, BLAST and ClustalW, are introduced here.

DOI of Published Version



Cold Spring Harb Protoc. 2016 Nov 1;2016(11):pdb.top093070. doi: 10.1101/pdb.top093070. Link to article on publisher's site

Journal/Book/Conference Title

Cold Spring Harbor protocols

Related Resources

Link to Article in PubMed

PubMed ID