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 and click Finish. 'Mixed sequence alignments' file is created.
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
Current Version is 2.12.10 (released August 20, 2018)
Downloads
- FTP site for all downloads
- Windows
- Mac OS X 10.10+ (Yosemite, El Capitan, Sierra, High Sierra)
- Linux (Ubuntu 18.04 "Bionic Beaver")
- Linux (Ubuntu 16.04 "Xenial Xerus")
- Linux (OpenSUSE Leap 42.3)
- Linux (Fedora 28)
- Linux (Fedora 27)
- Linux (Debian 9 "Stretch")
- RPM Installation key
- Source
- Older Versions
General
Help
Tutorials
- Basic Operation
- Using Active Objects Inspector
- Working with Non-Public Data
- Working with Multiple Views
- Broadcasting
- Genes and Variation
- Generating Sequence Overlap Alignments
- Working with BAM Files
- Loading Tabular Data
- SNP Table View
- Sequence View Markers
- Projects and Workspaces
- Publication quality graphics (PDF image export)
- Create Protein Alignments using ProSplign
- Exporting BAM/cSRA Coverage Graphs as WIG Files
- GFF-CIGAR export for alignments
- Exporting Tree Nodes to CSV
- Generic Table View
- Running BLAST search against custom BLAST databases
- Using Phylogenetic Tree
- Coloring methods in Multiple Alignment View
- Displaying translation discrepancies
- Graphical View Navigation and Manipulation
- Video Tutorials
Manuals
- Tree Viewer Formatting
- Tree Viewer Broadcasting
- Genome Workbench Macro
- Query Syntax in Genome Workbench and Tree Viewer
- Multiple Sequence Aligners