An interactive, graphical annotation tool.

Otter enables human annotators to compare numerous sources of evidence and then to build gene objects with multiple alternative transcripts. Otter works in symbiosis with the ZMap genome browser and the SeqTools suite to provide a complete integrated annotation workbench.

The principal users of Otter are the annotators of the HAVANA group, but it is also used by annotators around the world.

Otter orchestrates, enables and validates the annotation process. Annotation is stored in 'otter' databases which use an extended EnsEMBL schema.

All of Otter's interactions with the otter databases and with external data sources are carried out over the Internet using HTTP, which allows annotators to work anywhere in the world.

Much of the annotation produced by Otter is published via the VEGA database and website.

  • Browse by species, chromosome and clone.
  • Powerful search by gene, clone or evidence name or alias.
  • Flexible selection of evidence columns.
  • Transcript building by cut-and-paste of evidence.
  • Validation of splicing, translation and biotype.
  • Annotation by controlled vocabularies and by free-form comments.
Evidence sources
  • Local databases storing results of our analysis pipelines alongside the otter databases.
  • Databases maintained by the EnsEMBL team.
  • DAS sources.
  • Databases in PSL (UCSC / blat) format.
  • BAM files.
Supported platforms

Currently supported platforms are Linux and Mac OS X (Intel).

Download and Installation

Mac OS X
Sanger deskpro machines
The Otter client is available on any up-to-date internal Linux machines. Your path should contain /software/anacode/bin and the command is otter.
We regret that we do not have the resources to assist with Linux installations beyond the Sanger Institute.
Source code
Available from GitHub, but this is only the application core and there are many prerequisites.
Sanger Authentication

In order to use the system, users without a Sanger UNIX account (i.e. users who are not employed by the WTSI) will need to set up a Sanger website "Single Sign-On" account:

Mac OS X

Installation instructions are provided in the 'ReadMe' file contained in the disk image.

Learn and Support

A user manual is available, written by Charlie Steward.

License and Citation

Otter is free software and is distributed under the terms of the GNU General Public License.

Otter should be credited to "Genome Research Ltd."


Otter is maintained by the Annosoft team at the Sanger Institute.

If you have a bug or feature request, please raise a ticket by emailing anacode.

For any other enquires, please email the Annosoft team.


Sanger Contributors


  • Meeting report: a workshop on Best Practices in Genome Annotation.

    Madupu R, Brinkac LM, Harrow J, Wilming LG, Böhme U et al.

    Database : the journal of biological databases and curation 2010;2010;baq001

  • Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

    Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G et al.

    BMC genomics 2009;10;606

Tool type
  • Otter species, assemblies and columns

  • Otter assembly window

  • Otter session window

  • Otter transcript window

  • Otter transcripts, translation and evidence

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