WebApollo
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Application data |
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| Biological application domain(s) | Genomics, Sequence annotation, sequence functional annotation |
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| Principal bioinformatics method(s) | Annotation |
| Created at | Berkeley Bioinformatics Open-source Projects (BBOP) at Lawrence Berkeley National Lab; JBrowse project, Holmes Lab, UC Berkeley; Elsik Lab, University of Missouri. |
| Maintained? | Yes |
| Input format(s) | GFF3, BigWig, BAM |
| Output format(s) | GFF3, BED |
| Software features | Real time updating; lazy-loading; sequence visualization; sequence annotation |
| Programming language(s) | JavaScript, Perl, Java |
| Software libraries | Struts |
| Licence | Open Source |
| Operating system(s) | Requires Tomcat server |
| Contact: | apollo@lists.lbl.gov |
Summary: WebApollo is a browser-based tool for distributed community annotation of sequences.
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Description
WebApollo is a browser-based tool for visualisation and editing of sequence annotations. It is designed for distributed community annotation efforts, where numerous people may be working on the same sequences in geographically different locations; real-time updating keeps all users in sync during the editing process.
The features of WebApollo include:
- History tracking, including browsing of an annotation's edit history and full undo/redo functions
- Real time updating: edits in one client are instantly pushed to all other clients
- Convenient management of user login, authentication, and edit permissions
- Two-stage curation process: edit within a temporary workspace, then publish to a curated database
- Ability to add comments, either chosen from a pre-defined set of comments or as freeform text.
- Ability to add dbxrefs [database crossreferences] -- e.g. for GO functional annotation
- Can set start of translation for a transcript or let server determine automatically
- Flagging of non-canonical splice sites in curated annotations
- Edge matching to selected feature: matching edges across annotations and evidence tracks are highlighted
- Option to color transcript CDS by reading frame
- Loading of data directly from GFF3, BigWig, and BAM files, both remotely and from user's local machine.
- Configurable heat map rendering of BigWig data
- Per-session track configuration to set annotation colors, height, and other properties
- Export of annotation tracks as GFF3 and optionally other formats
- Search by sequence residues using server-side interface to BLAT or other sequence search programs
WebApollo is built on the sequence browser JBrowse and is part of the GMOD toolkit of free, open-source genetics and genomics software.
Links
References
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