MicroScope Platform Overview
- Overview of the annotation editor
- Annotation Rules
- BLAST results
- Compositional features
- E. coli K12
- B. subtilis
- MaGe/Curated annotations
- Syntonome / Syntonome RefSeq
- Similarities SwissProt / TrEMBL
- Predicted MetaCyc Pathways
MicroScope - Tutorial » MaGe » Genome Browser » Overview of the Genome Browser
Organisation of the genomic map
The MaGe genome browser is organised into 3 parts:
The predicted CDSs are indicated by rectangles on each frame.
The blue lines symbolize the coding prediction curve. They increase when coding probability is high and drop when the coding probability is low.
What is the meaning of the Genomic Object color code ?
The rectangles symbolising each Genomic Object (CDS, RNA...) follow a color code that corresponds to their annotation status, summarized below:
How to move along the sequence ?
Why sometimes genes are framed with a black line?
This is a way to quickly identify a specific gene when annotator use the Move To functionalities:
After a Move To action, the Genome Browser will be reloaded and centered around the corresponding gene, which will be framed with a black line.
How to read the table of annotated genomic objects ?
What is the Matrix ?
For a given genome several gene Matrices can be built for gene detection. You can select a given matrix be using the Matrix menu located below the genomic map. Then click on View: the Coding prediction curves are updated.
How to access a gene’s information ?
How to access the annotation history of a genomic object ?
Click on the History icon in located the table of genomic objects or in the Gene Annotation Editor window toolbar. The history opens in a new window, allowing you to follow the annotation’s evolution as well as the identity of previous annotators. You can send an email to an annotator by clicking on his/her login name.
How to use the "Export to Gene Cart" button ?
The Export to Gene Cart button allows you to export all genomic objects contained in the genomic map to a Gene Cart. If you click on the button, a new window opens, offering the choice of creating a new cart or to selecting a pre-existing cart in which store the data. You can access to your gene carts via the Gene Cart Interface.
Can I create a new genomic object ?
The NEW button located below the genomic map allows you to create a new genomic object. If you click on the button, a Genomic Object Editor window opens. You have to manually fill in all fields to create your new object. You have to specify its Type, Begin, End, Frame, Mutation, Product, ... Then click on SAVE.
Which program is used to detect the repeats ?
Repeat detection is performed by the Repsek program.
How to read the Repeat Regions table ?
If you click on a repeat region label, you obtain the detailed list of the repeat units contained in the repeat region in a new window.