Welcome to DNA Subway Classroom-friendly Bioinformatics.

Welcome to DNA Subway

Classroom-friendly Bioinformatics

DNA Subway

Commonly used bioinformatics tools in streamlined workflows

Teach important concepts in biology and bioinformatics

Inquiry-based experiments for novel discovery and publication of data

DNA SubwayRed Line: Genome annotation

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• Analyze up to 150 KB of DNA sequence

• De novo gene prediction

• Construct evidence-based gene models

• Visualize genome sequence in browser

DNA SubwayYellow Line: Genome prospecting

Yellow Line

• Analyze DNA or protein sequence

• Search plant genomes using TARGeT

• Explore gene duplications, transposons, and non-coding sequences not detectable in conventional BLAST searches

DNA SubwayBlue Line: DNA barcoding, and phylogenetics

Blue Line

• Analyze DNA or protein sequence

• Analyze DNA Barcoding sequence to identify plant, animal, and fungal species

• Generate phylogenetic trees and publish sequence to GenBank

DNA SubwayGreen Line: Transcriptome analysis

Blue Line

• Examine RNA-Seq data for differential expression

• Use High-performance computing to analyze complete datasets

• Generate lists of genes and fold-changes; add results to Red Line projects

Annotate Genome Sequence

Detect Genes and Build Gene Models

DNA Subway: Red Line


Requires JAVA 6 or above

www.java.comCheck your web browser has java enabled

Log in to DNA Subway

Create a project

Detect all the genes present

Import data from BLAST results and visualize in local browser

Construct a gene model

Verify gene model at Phytozome

Task: Analyze a ~3KB sequence from Chromosome 1 of A.thaliana

DNA SubwayRed Line: Demo analysis – determine a structure for an Arabidopsis gene

Create a Red Line project



Red Line

1. Click the Red Square to begin a project

2. Choose Plant and select Dicotyledon

3. Select sample sequence Arabidopsis thaliana (mouse-ear cress) Chr1, 3.40kb

4. Name the project and click Continue

Detect genes in the project sequence


DNA Subway

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5. Click Sequence to view the input sequence

Red Line: Demo analysis – determine a structure for an Arabidopsis gene

DNA Subway

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6. Click Repeat Masker

7. When View icon ( ) appears; click Repeat Masker again to examine results


DNA Subway

Tip: Before gene prediction, RepeatMasker attempts to identify repetitive sequences such as low-complexity, simple repeat, AT/GC-rich, or several types of transposons. Results are presented in a table. The Attributes column describes what type of repeat was detected in the ‘description=‘ field

AT-rich sequence at 1667bps


DNA Subway

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8. Click 1 or more gene predictors (Augustus, FGenesH, SNAP, tRNA Scan)

9. When View icon appears, click the gene predictor again to examine the results


DNA SubwayTip: de novo gene predictors predict genes within a given sequence. Each program is optimized differently; each program’s results vary. The Attributes column details features that make up a single predicted gene (e.g. the whole gene, mRNA, CDS, and exons). Sub-features are listed in the Type column.


Augustus predicts a single gene (designated ‘g1’) with 4 exons

Import data from BLAST results and visualize in local browser



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10.Click BLASTN to search and import similar DNA sequences

11.Click BLASTX to search and import similar sequences based on protein evidence

12.When the searches complete; click again to examine results

DNA SubwayTip: BLAST results are derived from UNIGENE or UNIPROT databases, and contain experimentally derived evidence (e.g. cDNAs) that can be used to infer a probable gene structure. The Attributes column has details on the sequence matches that were found (e.g. gene name, GenBank IDs, etc.)



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13. Click Local Browser to visualize results

DNA SubwayTip: You can use the local browser (Gbrowse) at any time to visualize the results of any tool’s output.


Construct a gene model



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14. Click on Apollo to start the program


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15. Hide the reverse strand; click the View menu and select Hide Reverse Strand

16.Expand tiers; click the Tiers menu and select Expand all tiers

17.If there are too many tiers displayed, click the Tiers menu; select Show Types Panel and uncheck Show evidence you wish to hide


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18. Double-click the Augustus model and drag into workspace

19.Double-click the new temporary model; right-click to open the Annotation info editor

20. Name the model ‘Augustus1’ in both ‘Symbol’ fields.


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21. Double-click the BLASTN model and drag into workspace

22.Double-click the new temporary model; right-click to open the Annotation info editor

23. Name the model ‘BLASTN1’ in both ‘Symbol’ fields.


Red Line23. Zoom in to examine the 5’ and 3’ ends of the gene models

24.Double-click the Augustus1 model and right-click to open the Exon detail editor

25. Adjust the 5’ and 3’ of the Augustus1 model to match the evidence provided by the BLASTN1 model

DNA SubwayTip: The BLASTN evidence is most useful for determining the transcript length (e.g. the 5’ and 3’ ends).



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26. Use any other available evidence* (e.g. BLASTN, User BLAST(N/X) ) to make alternative models if supported

27. Use the BLASTX evidence to determine start/stop codons. Drag any needed stop and start codon into your model.

*If you have hidden evidence, show it again from the show types panel in the Tiers menu


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28.Delete the BLASTN1 model and any other extraneous models

29.Save your work back to DNA Subway; click the File menu and select Upload to DNA Subway; close Apollo

Verify gene model at Phytozome



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30.Click Phytozome Browser and compare the created model(s) to the accepted transcript(s)

DNA Subway

Tip: Phytozome accepted transcripts are only available for DNA Subway sample sequences.


Welcome to DNA Subway Classroom-friendly Bioinformatics.

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