Support for Genome Workbench will end on March 31 2024. You may still use the application, but supporting documentation will not be available after this date. Read more.
How to use multiple sequence aligners in GBench
For multiple alignment creation Genome Workbench Tool includes four different third party alignment programs:
- CLUSTAL (omega and classical): http://www.clustal.org/
- Kalign: http://msa.sbc.su.se/cgi-bin/msa.cgi We found that kalign version 2.04 that we used does not compile on Windows. We had to make minor technical modifications to port it. NCBI modified source code and binaries are available at https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/kalign.
- MUSCLE: http://drive5.com/muscle/
- MAFFT: http://mafft.cbrc.jp/alignment/software/
Multiple sequence alignment creation
- Create set of DNA or protein sequences in fasta format Example fasta files:
- DNA: 16SRNA_Deino.fa (88 sequences)
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Proteins: Cu_Zn_SOD.fa (60 sequences)
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Upload fasta file into a new project via File > Open > File Import, select FASTA sequence files for file format, select path to the fasta file > Next > Use default settings > Next > Create a new Project_(add checkmark to "Create a Folder for the items" checkbox and specify subfolder name)> Finish.
- Select all objects (Shf+click) in newly created subfolder or Data folder in the Project view and open Tools menu (use double click, or Tools icon, or Right Click/Run Tool option).
- In Run Tool dialog select preferable multiple sequence aligner and click next.
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Run Tool dialog for selected aligner opens with all sequences selected (if sequences are not selected use Select All button).
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Select local path to the aligner executable. For the external tools such as aligners you need to download and install the tools from their corresponding sites. For many tools binary executables are available for all popular platforms.
- Click Finish and wait for alignment creation. Since alignment algorithm runs as an external process, command prompt window will pop up with the tool running.
- Created alignment will be automatically added to the Tool Results subfolder in the current project.
After multiple alignment has been created, it can be opened in the Multiple alignment view (see below) or/and used for tree construction, see How to create phylogenetic tree in GBench.
Open Alignment in Multiple Alignment view
Double click on alignment in Project View (or select it by right click, it will open Right click menu). In the menu select Open New View, in Open View dialog select Multiple Alignment View, and click Next to open alignment.
The image below demonstrates protein alignment created by MUSCLE.
Coloring is disabled by default. To select coloring method perform right click anywhere in the alignment, it will open menu, select Coloring > Select Method
In the Alignment Scoring Methods dialog select preferable method.
The image below shows protein alignment created by MUSCLE and colored using Rasmol amino acid colors.
The image below shows DNA alignment created by Kalign and colored by Frequency-Based Difference method.
Examples for all aligners can be seen in the saved projects:
Export of alignments to FASTA alignment file
You can export the alignment in FASTA format.
- Select the alignment object in your project (Project View)
- Use File->Export menu or context menu Export
- Use Export Dialog to export as FASTA Alignment file and specify the filename
See also
Multiple Sequence Aligners in Genome Workbench video tutorial
Coloring methods in Multiple Alignment View tutorial
Current Version is 3.8.2 (released December 12, 2022)
General
Help
Tutorials
- Basic Operation
- Using Active Objects Inspector
- Configure tracks and track display settings
- Working with Non-Public Data
- Viewing Multiple Alignments and Trees
- Broadcasting
- Genes and Variation
- Generating and Viewing Sequence Overlap Alignment
- Working with BAM Files
- Loading Tabular Data
- Working with VCF Files
- Sequence View Markers
- Opening Projects in Genome Workbench
- Publication quality graphics (PDF/SVG image export)
- Editing in Genome Workbench
- Create Protein Alignments using ProSplign
- 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
- Searching in Genome Workbench
- Graphical View Navigation and Manipulation
- Using the Text View to Review and Edit a Submission
- BAM haplotype filtering
- Displaying new non-NCBI molecules with annotations
- Creating phylogenetic tree from precalculated multiple alignment
- Creating phylogenetic tree starting from search
- Video Tutorials
General use Manuals
- Tree Viewer Formatting
- Tree Viewer Broadcasting
- Genome Workbench Macro
- Query Syntax in Genome Workbench and Tree Viewer
- Multiple Sequence Aligners
- Running Genome Workbench over X Window System
NCBI GenBank Submissions Manuals
- Table of Contents
- Introduction
- Genome Submission Wizard
- Save Submission File
- Reports
- Import
- Sequences
- Add Features
- Add Publication
- Comments
- Editing Tools