Running BLAST search against custom BLAST databases

Introduction

This tutorial will demonstrate how to run protein BLAST search against the local protein database.

You need to download and unzip the test data files for this tutorial. Please note the path to the location of saved files for later use.

For your custom database, first run makeblastdb on your FASTA file. Makeblastdb is part of standalone BLAST. See the links at the end of this tutorial.

Step 1: Load the test file

In Genome Workbench in File drop down menu select Open item. 'Open' dialog will display.

Select the File Import tab on the left. Leave File Format as 'Autodetect format'. Leave the 'Veify that the data match the selected file format' check-box checked.

Click on the folder icon next to the Filenames box, browse to the test files location and select the query_prot_dnaA_Sta.fa file.

Click Next, Next, and Finish.

Genome Workbench will add the new project.

Step 2: Run BLAST tool

Select the new project in Project View.

In the Tools drop down menu select the Run Tool item. 'Run Tool' dialog will be displayed.

Select the BLAST command and click Next.

In the 'Run Tool - BLAST' screen select:

• Query Sequences: Proteins
• Program: Protein-Protein (BLASTp)
• Subject: Local Database
• Database: \full path to database location that you have created during introduction\proteins_10_Sta_local_ids
• Add Local BLAST DB data loader to the project check box: checked

Click Next, observe default parameters and click Next again, observe default parameters, remove checkmark from the Link related hits together checkbox, and click Finish. 'Mixed sequence alignments' file is created.

Note: If the Link related hits together option is selected, blast result will be shown as a set of files, where each file contains separate alignment(s) for the different ranges of the query. These files can be analyzed (merge and remove redundancy) by the Clean Up Alignments tool.

Right-click the 'Mixed sequence alignments' file and select the Open New View command. Open View dialog will be displayed.

Select 'Multiple Alignment View' and click Next. Multiple alignment view will be displayed.

Other Information Sources

Genome Workbench also allows to run nucleotide BLAST search against local nucleotide database (MEGAblast and blastn), protein against translated nucleotide database (tblastn), translated nucleotide against translated nucleotide database (tblastx), and several other.

For more information please refer to:

• BLAST setup
• BLAST download and executables
• Manual
• Building a database with local sequences
• Send your command-line BLAST questions to Blast-help@ncbi.nlm.nih.gov