Start using MYPalmViewer

Accessing MYPalmViewer

The MyPalmViewer is an interactive genome browser designed to visualize oil palm genomic features such as genes, SNP markers, scaffolds, and annotations from the EG11 reference genome and related assemblies. Follow the steps below to explore and analyze the genome data efficiently. 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

Select the Genome Assembly

Use the Assembly selector (top-left corner) to choose from available genome builds:

1. EG11 (Elaeis guineensis)
2. EG5.1
3. Other species (if available, e.g. E. oleifera)

The browser will automatically reload with the selected assembly.

Navigate to a Chromosome or Scaffold

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.

Track available

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.

Custom tracks

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.

BLAST

The BLAST results show an option to view the result in MYPalmViewer.