Protocol

Sequence Alignment and Homology Search with BLAST and ClustalW

  1. Zhiping Weng

Abstract

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.

Footnotes

  • From the Molecular Cloning collection, edited by Michael R. Green and Joseph Sambrook.

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This Article

  1. Published in Advance August 29, 2016, doi: 10.1101/pdb.prot093088 Cold Spring Harb Protoc 2016: pdb.prot093088- © 2016 Cold Spring Harbor Laboratory Press
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