GMOD: Genomics Resources forEmerging Model Organisms

AbstractAs genomics technologies have become widely available, manyemerging model organism communities have accumulated anunprecedented volume of data on sequences, genotypes, expressionpatterns, etc. Much of this data is from organisms well suited tocomparative genomic, evolutionary and ecological studies. Moredata offers more potential for discovery, but it also makes it isharder to organize, visualize and annotate. GMOD is a collection ofinteroperable open source software, including tools for managing,annotating and visualizing genomic data. GMOD tools are used indiverse contexts, from genome annotation projects withinindividual labs to major model organism databases.

Comparative GenomicsGMOD supports visualizing compara-tive genomics data. Sybil displayssyntenic regions and whole genomecomparisons. CMap shows compara-tive maps of any type (genetic,physical, sequence, …). SynView,GBrowse_syn and SynBrowse areGBrowse-based synteny browsers.

Dave Clements, Hilmar Lapp, Todd J. VisionNational Evolutionary Synthesis Center (NESCent), Durham, NC, USA

http://nescent.org clements@nescent.org

The GMOD Help Desk is hosted by NESCent and is funded byNational Institutes of Health grants to Ian Holmes at UC Berkeley

and James Hu at Texas A&M.

Getting Started with GMOD

Start at GMOD.org

Download Software

FAQs and HOWTOs

Project Events

Project News

Contribute Doc!GMOD.org is a Wiki

Support: Help Desk& mailing lists

Contribute Code!We’re open source

Popular GMOD Components

http://gmod.org

GMOD for Biologists

GBrowse Genome Browser

GBrowse is a web-based viewer fordisplaying genomes and their

annotation. It is highly configurable byend-users and site administrators. Ifyou have sequence and/or genomic

annotation, GBrowse can show it.

Apollo Genome EditorThe Apollo genome editor is used toannotate genomic sequences. Apollosupports adding new annotations andrefining computational annotations.It is used in several communityannotation efforts.

Chado Database SchemaChado is the unifying data model for GMOD. It is a modular andextensible database design for biological data. Chado supportssequence, genetic, phenotypic, ontology, gene expression, andmany other datatypes.

GMOD records behaviors asphenotypes by combiningontologies such as GO andPATO (the Gene and Phenotypeontologies) in Chado, GMOD'sdatabase schema. These canthen be displayed or queried.You can also use (or create)more specific ontologies suchas the Social Insect BehaviorOntology (SIBO) or anatomyontologies for specificorganisms.

TextPresso, PubSearchChado Publication Module

Curate/searchOrganize

Publications

Java TreeView, Caryoscope,GeneXplorerChado Mage, Expression Modules

View

Organize

Microarray andExpression

Chado Genetics ModuleGMODWeb

OrganizeView

Phenotype,Genotype

Chado Organism, Phylogeny modulesGMODWeb

OrganizeView

PhylogeneticTrees

Pathway ToolsView, predict,organizePathways

Chado CV moduleGO Term Viewer

CurateView

Ontologies

CMap, SynView, SynBrowse, SybilSybilChado Map Module

ViewAnnotateOrganize

Comparative,Synteny

GBrowseApolloChado Sequence Module

ViewAnnotateOrganize

GenomicSequence

then GMOD can help with& you need toIf you have

What Can GMOD Do?

Chado has recently been extendedwith the Natural Diversity module,which supports stocks, individuals,pedigrees, crosses, geolocations,and phenotype and genotypeexperiments. Taxonomy andphylogenetic trees in Chado’s coremodules have also beenrationalized.

Behavior and Phenotype in GMOD

An allele page at ParameciumDB showingphenotype information integrated withsequence, genetic, and stock data.

Natural Diversity in GMOD