Advantages of using SeqNinja files

SeqNinja is DNASTAR’s tool for advanced and batch editing of genome sequences and features. SeqNinja allows you to convert file formats, batch edit and export features, merge and split sequence data, and transfer features between genome versions, automating the process of adjusting sequence coordinates between SeqMan NGen assemblies. The SeqNinja project – which can be created easily using the provided templates – has the extension “.star,” and uses one or more data files as inputs for its calculations. When you run the .star program, the output format can be saved in a variety of popular file types, such as FASTA, GenBank, Lasergene, etc.

While you can certainly add the SeqNinja output files to MegAlign Pro, it is also possible to add the .star project as input. To add either of these, see Add ungapped sequences to a project.

Adding one or more SeqNinja projects (.star) to a MegAlign Pro project is an indirect way of adding sequences. Sequences specified by a SeqNinja project file are all those that would be written if the project were run using SeqNinja. Using SeqNinja project files as MegAlign Pro input can save a lot of time and effort. The advantage of adding a .star project to MegAlign Pro is that it will always call up the most up-to-date version of the input data for use in making its output. So if you change, add, or delete the input data that the .star file points to, the .star file will update this information in MegAlign Pro.

The following example demonstrates the advantages of adding a .star file to MegAlign Pro:

Assume you have a directory of genomes for a phylogenetic study. You want to extract a specific gene, or set of genes, from each genome to build an alignment, and then a phylogenetic tree. Over the course of your work, new genomes and new versions of existing genomes become available. You want to generate a current alignment and tree that reflects those additions or changes. Here are three scenarios of the steps needed to do this:

Good: Without using SeqNinja:

1. Manually extract the genes of interest.

2. Generate output files (e.g., FASTA, GenBank, etc.).

3. Add the files to MegAlign Pro.

4. Run the alignment.

5. Repeat Steps 1-4 every time the input data changes.

Better: Using SeqNinja output (e.g., FASTA, GenBank) or a SeqNinja project file as MegAlign Pro input:

1. Create a SeqNinja program to automatically extract the genes of interest.

2. Run the program and generate output files (e.g., FASTA, GenBank, etc.).

3. Add the output files or the SeqNinja project (.star) to MegAlign Pro.

4. Run the alignment.

5. Repeat Steps 2-4 every time the input data changes

Best: Creating a SeqNinja project to use with MegAlign Pro:

For detailed information about creating SeqNinja projects, launch the SeqNinja application and select Help > Help Contents.

When you use a SeqNinja Project (.star) file as input for MegAlign Pro, note that the project is read as a “set of sequences,” and is not actually executed, meaning no sequence files are written. This type of project has the following limitation:

Any input files referenced in the program must already exist. In other words, the program should not reference an input file that doesn’t exist until it is created earlier in the same program. Instead:

• Replace all the references to the input file with a variable (e.g., $A), or…

• Create a SeqNinja program to create the necessary files and run the program. Then, in the SeqNinja program you wish to add to MegAlign Pro, reference those already-created files.