Sequence alignment and homology search with BLAST and ClustalW

Jui-Hung Hung, Zhiping Weng

Research output: Contribution to journalArticlepeer-review

69 Scopus citations


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.

Original languageEnglish
Pages (from-to)1016-1021
Number of pages6
JournalCold Spring Harbor Protocols
Issue number11
StatePublished - 1 Nov 2016


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