piBROWSE: Visualize piRNA Annotations across Genome

Genome AssemblyChromosomePosition

Select Annotation Tracks

piRNAsPing Pong piRNAs
piRNA Clusters Unique piRNA
RefSeq Transcripts
RefSeq Genes
MPromDB Promoter
CpG Islands
Premature & mature miRNAs
Pseudogene
Repeat Masker 3.27 Repeats
Ensembl Long Non-coding RNA

Using piBROWSE

  • Moving
  • Move the view by clicking and dragging in the track area, or by clicking or in the navigation bar, or by pressing the left and right arrow keys.
  • Zooming
  • Zoom in and out by clicking or in the navigation bar, or by pressing the up and down arrow keys while holding down "shift".
  • Showing Tracks
  • Turn a track on by dragging its track label from the "Available Tracks" area into the genome area, or double-clicking it. Turn a track off by dragging its track label from the genome area back into the "Available Tracks" area.
  • Searching
  • Jump to a feature or reference sequence by typing its name in the location box and pressing Enter. Jump to a specific region by typing the region into the location box as: ref:start..end.
  • Example Searches
  • uc0031k.2 searches for the feature named uc0031k.2. chr4 jumps to chromosome 4 chr4:79,500,000..80,000,000 jumps the region on chromosome 4 between 79.5Mb and 80Mb. 5678 centers the display at base 5,678 on the current sequence

    References:

  • Skinner ME, Holmes IH. Setting up the JBrowse genome browser. Curr Protoc Bioinformatics. (2010).
  • Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: a next-generation genome browser. Genome Res. (2009).