DNA Subway

Gene prediction, homolog identification, species classification, RNA-Seq analysis, and microbiome profiling through five integrated genomics workflows.

Solution by CyVerse

Overview

DNA Subway is an educational bioinformatics platform developed by CyVerse that bundles research-grade bioinformatics tools, high-performance computing, and curated databases into accessible genomics workflows. Designed with a fun and intuitive interface, it is ideal for students, educators, and researchers who want to learn, teach, or perform high-level genome analysis without requiring deep computational expertise.

Users navigate the platform by "riding" five distinct workflow lines, each targeting a specific area of genomic analysis. From gene prediction and annotation to microbiome profiling, DNA Subway makes powerful open-source bioinformatics tools approachable through a sequential, logical workflow structure.

Available Workflow Lines

Red Line: Predict and annotate genes in up to 150,000 base pairs (150kb) of DNA sequence.
Yellow Line: Prospect entire sequenced genomes to identify homologs and related genes and sequences.
Blue Line: Identify species using DNA barcodes, determine sequence relationships, and visualize phylogenetic trees.
Green Line: Analyze RNA-Seq datasets to examine differential transcript abundance and gene expression.
Purple Line: Analyze metabarcoding and environmental DNA (eDNA) samples using QIIME2 for microbiome studies.

Key Features

Research-grade bioinformatics tools organized into sequential, logical workflows presented as subway lines for ease of navigation.
A friendly interface that introduces users to the same open-source bioinformatics tools used by professional researchers.
Support for both sample datasets and reference data, as well as the ability to upload custom data collections.
A companion site offering in-depth wet lab protocols and student barcoding projects through the DNA Barcoding 101 resource.

Learning and Teaching Resources

Comprehensive manuals, guides, and tutorials to support self-directed learning and classroom instruction.
A video tour to help new users get oriented with the platform quickly.
Suitable for teaching students to analyze DNA using professional bioinformatics tools in an accessible environment.

DNA Subway is part of the broader CyVerse Open Science Workspace and is available to users with a CyVerse account. It is backed by CyVerse's high-performance computing infrastructure, enabling scalable analysis for both educational and research purposes.