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4.1. What Are Annotations?
An Annotation in Genboree is a coordinate range on a defined Entry Point (such as a chromosome). Examples include: exons, chromosome bands, mapped BACs, repeat regions, promotor sites, base-conservation scores, etc.
Genboree also has the concept of Annotation Groups, which are sets of linked annotations that are best displayed via group-aware drawing styles. For example, the exons of a gene transcript should always grouped together. Other examples include mate-pair reads, the HSPs of a significant BLAST/BLAT hit, etc.
More information about Annotation Groups is provided in the description of the name column.
An Annotation also has other attributes associated with it, such as an orientation, a type / subtype, a score, and possibly even user-defined attributes. For more information, please refer to "5. The LFF Annotation Format".
4.2. Uploading Annotations:
To upload annotations to your Genboree database:
NOTE: if you have errors in your file, you will receive an email indicating the offending line numbers and the problem(s) on those lines.
NOTE: if you have a slow Internet connection, or a huge number of annotations to upload, you may want to (a) split the file and upload each piece and/or (b) compress the file with either Gzip or Zip (e.g. WinZip).
NOTE: The checkbox indicated by the red arrow (←) in the image above, causes ALL the annotation tracks currently in the database to be deleted before your file is processed. This is useful for replacing an entire database with a new set of fresh data in a single step, for example.
4.3. Annotation File Formats:
4.3.1. LFF Annotation Format
This is the preferred annotation format, because it is the most expressive and feature-filled for Genboree. Particular fields and values in this format enable several features for capturing and displaying your annotation data in the most complete and customizable way.
The Genboree LFF format is adapted from the LDAS upload format described at http://www.biodas.org/. Although it is backwards compatible with the original, Genboree LFF includes some optional fields to support extra annotation information and browser capabilities.
Due to the importance of the LFF format within Genboree, please read "The LFF File Format" for a description of the format and how the columns relate to Genboree.
4.3.2. Other formats
Genboree also supports some other file formats:
However, such annotations undergo a generic conversion to LFF and may not
allow your data to be displayed how you wish or may not capture non-essential data
that normally would be accessible.