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2.1.1. What are "entry points"?
Entry points comprise the coordinate system on which annotations are made. For example, a chromosome is an entry point. For unassembled genomes, the scaffolds might be the entry points.
Entry points must be defined within Genboree, with a name and a length, so that annotations can be placed on them.
Currently, entry points are independent within Genboree; i.e. not directly linked. They are simply the names of chromosomes, scaffolds, etc, on which you will place your annotations.
2.1.2. What is a "genome" in Genboree?
A "genome" is a set of entry points. It is the complete set of valid chromosomes, or maybe scaffolds, upon which your annotations can be placed.
In fact, you could have a set of entry points from several species (for example, the X chromosomes of several mammals).
2.2. Methods for Defining a Genome:
When creating your Database, you will use the Reference Sequence droplist to choose to either upload your own entry point definitions or use a set of pre-existing entrypoints:
2.2.1. Use a template genome
For your convenience, Genboree provides some template genomes, which are predefined sets of entry points, for some of the fully assembled mammals. Simply select which template to use when you create your database (see image above).
These templates include entry point definitions for the assembled chromosomes, and often have sequence data and a few basic annotation tracks.
If you would like to have the unassembled portions of the chromosomes or additional annotation tracks included in a particular template definition, please email your request to us.
You can also add entry points to your Database at any time, by uploading your own entry point definitions .
2.2.2. Define a custom genome
Genboree lets you define your own "genome", perhaps for annotating a newly assembled (or partly assembled) species or for a special case not covered by an existing template.
When creating a Database for a custom genome, ** User Will Upload ** tells Genboree that you will be providing your own chromosome or scaffold definitions later (see image above).
Please refer to "3. Uploading Entry Points"
for more information about how to define and upload custom entry points to Genboree.