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Genomsawit Website
Official Portal Of
Malaysian Oil Palm Genome Programme (MyOPGP)
Malaysia MPIC MPOB

MYPalmViewer

MYPalmViewer is an oil palm genome browser developed to display and explore the chromosomes of the oil palm. This section provide a brief introduction on how to use MYPalmViewer

Accessing MYPalmViewer

MYPalmViewer can be access via a direct link from this webpage (this is for whole genome browsing) or via blast analysis.

  1. Direct Link to MYPalmViewer
  2. BLAST result

The interface of MYPalmViewer is shown below

Section Description
A Gbrowse main menu
Browser : Webpage to visualize the oil palm genome
Select tracks : Tracks representing the mapped sequences to the oil palm genome. It allows users to select specific tracks in the browser.
Snapshots : Save the current browser screen as a picture
Custom tracks : It allows users to add a customized track to oil palm MYPalmViewer
Preferences : User screen configuration setting of MYPalmViewer
B It allows user to search the browser based on keyword and location on the browser. The format for location search is start with the oil palm chromosome number (example: EG_Chr[1 to 16]), a colon (:), start location and end location with a double dot (..) separator.
Example: EG_Chr1:10..3000037
C Example of a browser view of a specific location in MYPalmViewer
D Scrool and zoom options in MYPalmViewer
E The selected tracks are visualize in section E.
As of August 2015, there are 12 categories of data tracks available in MYPalmViewer, which are listed below:

  1. Oleifera 8 Scaffolds
  2. Pisifera 5 Scaffolds
  3. GeneThresher (TM) Sequences
  4. Oil Palm Transcripts
  5. Oil Palm Protein Sequences
  6. P5 GlimmerHMM Gene Models
  7. Genetic Markers
  8. Uniprot Annotations
  9. Arabidopsis thaliana Genes
  10. Oryza sativa Genes
  11. Oil Palm Retroelements
  12. Scaffold Gaps
Also available are the DNA composition (GC Content) and restriction enzyme sites (Restriction Sites) of the P5-build.
MYPalmViewer allows user to upload own track data in six file format (BED, Gbrowse Feature File Format, GFF, GFF3, Wiggle (WIG) and BAM or SAM). Online data which can be reach through URL is also acceptable.
The blast result using EG5_Genes.v2.faa, EG5_Genes.v2.fna, P5_scaffolds.na and EG5_linked.na database will show an option to view the result on MYPalmViewer.


The mark "A" shows the link of the hit blast result to the browser.

  LINK

  Gbrowse