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Collaborative, instantaneous, web-
based, built on top of JBrowse.
Apollo supports curation of gene models for
multiple or...
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Apollo Genome Annotation Editor: Latest Updates, Including New Galaxy Integration

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Manual curation is crucial to improving the quality of the annotations for a genome sequencing project. During this portion of the genome sequencing workflow, curators use a variety of experimental evidence to improve on automated predictions to more accurately represent the underlying biology. 

Apollo is a web-based genome annotation editor that allows curators to manually revise and edit genomic elements. It provides a reporting structure for annotated genomic elements and an ‘Annotator Panel’ that allows users to quickly browse the genome and all available annotations. Users can manually edit the structure of a genomic element as well as add metadata, including references to other databases, adding functional assignments to genes and gene products with specific lookup support for Gene Ontology (GO) terms, as well as including references to published literature in support of these annotations.

Apollo is currently used in more than one hundred genome annotation projects around the world, ranging from the annotation of a single species to lineage-specific efforts supporting annotation for dozens of organisms at a time. Apollo enables collaborative, real-time curation (akin to Google Docs); researchers may restrict access to certain annotations depending on the role of users and groups within the community, as well as share tracks of evidence data with the public. Users are able to export their manual annotations via FASTA and GFF3 files, the Chado database schema, and web services. The news hot of the presses is that Apollo is now available for integration with Galaxy via Docker! This allows users to run analyses on their genome of interest, including a step of manual curation, all from the comfort of their installation of the versatile Galaxy platform.

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Apollo Genome Annotation Editor: Latest Updates, Including New Galaxy Integration

  1. 1. Collaborative, instantaneous, web- based, built on top of JBrowse. Apollo supports curation of gene models for multiple organisms in one server and generates analysis-ready data as well as progress reports. 1 2 3 1. User-created Annotations 2. Evidence Tracks: Experimental data, alignments 3. Annotator Panel: Removable dock 4. Tabs for searching, editing, and exporting Data 5. Switch between organisms and sequences 6. Visualize and edit annotation details 5 5 5 4 6 Latest Features {REST} Automated Annotations GFF3, FASTA, BAM, etc. GFF3, FASTA, Chado Next Workflowe.g. Tripal Manual Annotation 1. Import to JBrowse 2. Import Organism 3. Manual Annotation 4. Export Annotations Export and update a Chado database Annotate multiple organisms per server Change type of genomic element to annotate gene pseudogene ncRNA Galaxy / Apollo Integration 1 2 4 3 Example of Galaxy / Apollo Integration using Docker Folded 592 bp Bringing exons closer together facilitates annotating gene models with long introns. Web Services Client Perl, Shell, Groovy, PHP, etc. {JSON} GFF3 FASTA Annotators JBrowse Directories WebSockets {REST}and {REST} File System JDBC Apollo components Customizable Security Apollo Server - Grails Controllers Views (gsp) Services & Plug-in Domains SiteMesh (OpenSymphony) GORM Hibernate HSQLDB Java Enterprise Edition Groovy Java Virtual Machine Gant Scaffold 2Scaffold 1 Genome Assembly . . . . . . Scaffold n 212,500 214,000 GB40027-RA GB40022-RA GB40028-RA Scaffold 223 Scaffold 17 1,350,000 Scaffolddetails Scaffolddetails Annotation across scaffolds Artificially joining scaffolds facilitates annotation of gene models split across two or more scaffolds. Transforming Coordinates UNIVERSITY of MISSOURI Mónica C Muñoz Torres1, Nathan A Dunn1, Deepak Unni2, Eric Yao3, Eric Rasche4, Colin Diesh2, Christine E Elsik2, Ian Holmes3, Suzanna E Lewis1 1 Lawrence Berkeley National Laboratory, Genomics Division, Berkeley, CA. 2 University of Missouri, Divisions of Plant and Animal Sciences, Columbia, MO. 3 University of California Berkeley, Bioengineering, Berkeley, CA. 4 Center for Phage Technology, Texas A & M University, College Station, TX. GenomeArchitect.org github.com/GMOD/Apollo @apollo_bbop

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