MAKER PAG 2010 Workshop

View of [MAKER](MAKER.1 "MAKER") annotations in the [Apollo](Apollo.1 "Apollo") genome annotation curation tool. Supporting evidence is shown in the upper dark panel. Gene annotations are shown in the blue panel. [MAKER](MAKER.1 "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](GBrowse.1 "GBrowse") genome viewer, and manually updated using the [Apollo](Apollo.1 "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 - [Carson Holt](User%253ACarsonholt "User%253ACarsonholt"), University of Utah ## Tutorial Level **Beginner to Intermediate.** No prior knowledge of MAKER or genome [annotation](Annotation "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](GMOD_Components "GMOD Components") 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](PAG_2010 "PAG 2010") at PAG 2010, including - A [workshop](GBrowse_PAG_2010_Workshop "GBrowse PAG 2010 Workshop") on [GBrowse](GBrowse.1 "GBrowse"), a genome viewer. - A [workshop](GBrowse_syn_PAG_2010_Workshop "GBrowse syn PAG 2010 Workshop") on [GBrowse_syn](GBrowse_syn.1 "GBrowse syn"), a comparative genomics viewer built on [GBrowse](GBrowse.1 "GBrowse") - The Gramene Workshop will include a section on the [CMap](CMap.1 "CMap") comparative map viewer. See [PAG 2010](PAG_2010 "PAG 2010") for a more complete list of GMOD-related presentations at PAG XVIII. ## Navigation menu ### Navigation - [GMOD Home](Main_Page) - [Software](GMOD_Components) - [Categories / Tags](Categories) ### Documentation - [Overview](Overview) - [FAQs](Category%253AFAQ) - [HOWTOs](Category%253AHOWTO) - [Glossary](Glossary) ### Community - [GMOD News](GMOD_News) - [Training / Outreach](Training_and_Outreach) - [Support](Support) - [GMOD Promotion](GMOD_Promotion) - [Meetings](Meetings) - [Calendar](Calendar) ### Tools - Browse properties - Last updated at 18:54 on 8 October 2012. - Content is available under a GNU Free Documentation License unless otherwise noted.