MAKER PAG 2010 Workshop

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PAG 2009 MAKER: An easy to use genome annotation pipeline

January 9-13, 2010
Plant and Animal Genome Conference
San Diego, California, USA

This page provides additional information about the MAKER workshop at the Plant and Animal Genome XVIII Conference (PAG 2010) held in San Diego on January 9-13, 2009.


This presentation is now available online.


View of MAKER annotations in the Apollo genome annotation curation tool. Supporting evidence is shown in the upper dark panel. Gene annotations are shown in the blue panel.

MAKER is a portable and easily configurable genome annotation pipeline. It's purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain the gene prediction algorithms used by MAKER, producing higher quality gene-models on subsequent runs. MAKER's inputs are minimal and its outputs can be directly loaded into a GMOD compatible database. They can also be viewed in the GBrowse genome viewer, and manually updated using the Apollo genome annotation editor.

MAKER can be installed locally on your own machine, or for smaller datasets, you can upload your data to the online MAKER gene annotation web service. Examples in the workshop will focus primarilly on using the new MAKER web service, but will aslo touch on how to install and use MAKER on a local machine.

Workshop Instructor

Tutorial Level

Beginner to Intermediate. No prior knowledge of MAKER or genome annotation pipelines is required.

The tutorial is aimed at biologists who have, or soon will have, genomic sequence data.

This workshop will cover

  • Introduction to Genome Annotation
  • MAKER Overview
  • MAKER Web Interface
  • Creating an Account and Uploading Data
  • Basic Explanation on Using a Locally Installed Version of MAKER
  • Quick Demonstration on Loading MAKER Data into Other GMOD Tools

This is not a hands-on workshop. There are portions of the workshop for which the user may follow along online if they wish, but it is not necessary. After the workshop, the MAKER presentation and a VMware system image with MAKER prerequisite software already installed will be made available on this page. You can use this image to walk through the material presented at this workshop.

Other GMOD Presentations and Meetings

GMOD will have a strong presence at PAG 2010, including

See PAG 2010 for a more complete list of GMOD-related presentations at PAG XVIII.