DNA Subway Basics and Logging in to Subway¶
DNA Subway is designed to be a classroom-friendly approach to bioinformatics. Unlike most CyVerse platforms, you can even use Subway without registering for a CyVerse account. We do encourage you to register however, only work from registered users can be saved. DNA Subway uses the same open-source bioinformatics tools used by researchers. See a complete list of the tools provided in the Subway pipelines.
Some things to remember about the platform
Registered user and Guest user account types
- DNA Subway access must be requested through the CyVerse user portal. You can check if you already have access, or request access by logging into the portal and visiting the My Services page. If DNA Subway is not listed, click on Available services to request access.
- Guest users will not have their worked saved beyond a single DNA Subway session. They are also disallowed from using one of the gene predictors (FGenesH) in the genomic annotation pipeline (Red Line).
- We suggest that every student using DNA Subway obtain their own account.
Sample Datasets and reference data
All Subway lines accept user data and also have sample data that can be immediately used to create a project.
- Red Line - Genome Annotation: Samples of plant and animal genomes that can be used in annotation projects
- Yellow Line - TARGeT Search for transposons and other DNA Sequences: Several model plant genomes
- Blue Line - DNA Barcoding and Phylogenetics: Sample sequence from plant, animal, fungal, and bacterial barcoding regions; human mitochondrial DNA sequence
- Green Line - RNA-Seq for differential expression: Sample high-throughput reads from RNA-Seq experiments
If there is a reference data set or sample sequence you would like added, you can contact CyVerse using the DNA Subway Contact page
Public and private projects - DNA Subway projects are private by default, but can be shared by making them public. Public projects are searchable and are a great way to share data or present analysis for grading in a classroom project.
Logging into DNA Subway as a registered user¶
- Access the DNA Subway website at https://dnasubway.cyverse.org/
- If you wish to use DNA Subway as a guest click ‘Enter As Guest’
When using DNA Subway as a guest, you will be able to work only on the Red, Yellow, and Blue lines. Additionally, some Red Line functionalities will be disabled. Finally, after logging out, or a period of inactivity (>~ 30 min) you work will be discarded.
- Enter your CyVerse username and CyVerse password.