Sequence Alignment and Homology Search with BLAST and ClustalW

UMMS Affiliation

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

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Bioinformatics | Computational Biology


This protocol illustrates the steps of searching a sequence database with BLAST, which in essence performs pairwise alignment between the query sequence and each target sequence in the database. Steps for performing multiple sequence alignments with ClustalW are then described. Argonaute 2 (Ago2) is an essential component for small interfering RNA (siRNA)-directed RNA interference (RNAi) in fruit flies. This protocol uses Ago2 to demonstrate how to search for all Ago2 paralogs in the fly proteome using BLAST and to obtain a multiple sequence alignment of these sequences with ClustalW.

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Citation: Cold Spring Harb Protoc. 2016 Nov 1;2016(11):pdb.prot093088. doi: 10.1101/pdb.prot093088. Link to article on publisher's site

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Link to Article in PubMed

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Cold Spring Harbor protocols

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