Annotation
Supporting annotation of biological data is a central goal of GMOD.
Annotation can be done computationally or manually using community
annotation
or by dedicated curatorial staff.
This page is about creating annotations. GMOD also has a number of
solutions for visualizing
annotations.
Contents
Genome Annotation
Manual Genome Annotation
- Apollo is the manual genome annotation tool of
choice for GMOD users.
Computational Genome Annotation
“Genome annotation, not genome sequencing, is becoming the bottleneck in
genomics today.”
First line of the MAKER paper.
- MAKER is a pipeline for annotating eukayotic
genomic data.
- DIYA is a pipeline for annotation prokaryotic genomic
data.
- Ergatis is a
web-based utility for creating and running reusable computational
analysis pipelines.
- Galaxy allows users to search remote resources,
combine data from independent queries, and visualize/save the results.
- Genome grid project is a package of
genome data analysis with methods, protocols, and documentation.
Publication Annotation
- Textpresso is a text mining package for
biological literature.
Community
annotation
is an area of growing interest to the GMOD community.
- Apollo is used in several community annotation
efforts to maintain and curate genomic data.
- TableEdit is a popular
MediaWiki
extension for updating tabular and database data. Work is currently
under way to build a wiki front end to
Chado using
TableEdit.
Categories:
Navigation
Documentation