Title

Sequence Alignment and Homology Search with BLAST and ClustalW

UMMS Affiliation

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

Date

11-1-2016

Document Type

Article

Disciplines

Bioinformatics | Computational Biology

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.

Rights and Permissions

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

Related Resources

Link to Article in PubMed

PubMed ID

27574197