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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.

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

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.