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Walkthrough of DNA Subway Yellow Line - Sequence Detection

Genome prospecting uses a query sequence (DNA or protein of up to 10,000 base pairs/amino acids) to find related sequences in specific genomes or in a database. A major purpose of genome prospecting is to identify members of gene or transposon families. DNA Subway uses the TARGeT workflow, which integrates BLAST searches, multiple sequence alignments, and tree-drawing utilities. Yellow line uses TARGeT (Tree Analysis of Related Genes and Transposons) uses either a DNA or amino acid ‘seed’ query to: (i) automatically identify and retrieve gene family homologs from a genomic database, (ii) characterize gene structure and (iii) perform phylogenetic analysis. Due to its high speed, TARGeT is also able to characterize very large gene families, including transposable elements (TEs). [citation]

Some things to remember about the platform

  • Yellow Line will return sequences that would normally be excluded from a BLAST search of a genome (e.g. repetitive sequences, transposons).
  • Yellow Line is implemented only for plant genomes

DNA Subway Yellow Line - Create a Yellow Line Project

  1. Log-in to DNA Subway - unregistered users may ‘Enter as Guest’

  2. Click ‘Prospect Genomes using TARGeT’ (Yellow Square)

  3. Select a sample sequence, or paste in a sequence to search for.

    Note

    DNA Subway Yellow Line is only implemented to search a limited set of plant genomes.

  4. Provide your project with a title, then Click ‘Continue’

Example Exercise - Project Creation: mPing Mite element to search plant genomes for an active transposon

The mPing MITE element is an example of an active transposon in rice. Transposons are a major class of DNA elements that impact the function of the genome.

  1. Create a Yellow Line project following the steps above and using the mPing Mite Element (Oryza sativa/Rice)

DNA Subway Yellow Line - Search Plant Genomes with TARGeT

  1. Click and select the genome(s) you wish to search and the click; ‘Run’ to search those genomes.
  2. Click the ‘Alignment Viewer’ button to view the results of the search as a multiple alignment.
  3. Click the ‘Tree Viewer’ button to view a tree that will group results by similarity.

Tip

Alignment Viewer Generates an alignment of all search results

yellow_alignment

Tree Viewer Displays the results of sequence matches as a tree, grouped by sequence similarity

yellow_tree

Tip

Some Useful Definitions - Transposons (DNA, Retroviral, LINES): Genetic elements which have the ability to be amplified and redistributed within a genome. - Non-autonomous transposons: Transposons which lack an active transposase gene, thus requiring help from another transposon to move. - Autonomous transposons: Transposons which have a functional transposase and can move within the genome.

Example Exercise - Search Plant Genomes: mPing Mite element

  1. After loading the mPing Mite Element as the query, search the Oryza Sativa genome, and examine the results in the Alignment and Tree Viewers.
  2. Repeat this analysis with a new project using the Ping transposase gene and the Ping Transposase protein.

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