Otterlace

An interactive, graphical annotation tool.

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

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

[Genome Research Limited]

Information

otterlace - transcript

otterlace - transcript
Enlarge this image (1242 x 842)

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

All of Otterlace'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 Otterlace is published via the VEGA database and website.

Features

  • 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).

Licence

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

Screenshots

otterlace species, clones & columns

otterlace species, clones & columns
Enlarge this image (736 x 383)

assembly window

assembly window
Enlarge this image (873 x 671)

session window

session window
Enlarge this image (616 x 517)

transcript window

transcript window
Enlarge this image (407 x 637)

otterlace transcripts translation & evidence

otterlace transcripts translation & evidence
Enlarge this image (1242 x 842)

Download

Mac OS X
ftp://ftp.sanger.ac.uk/pub/anacode/otterlace/
Sanger deskpro machines
The Otterlace client is available on any up-to-date internal Linux machines. Your path should contain /software/anacode/bin and the command is otterlace.
Linux
Please contact anacode@sanger.ac.uk for more information about downloading and installing the Otterlace client for Linux.
Source code
Available from GitHub, but this is only the application core and there are many prerequisites.

Installation

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.

Documentation

User manuals

A user manual is available, written by Charlie Steward.

Publications

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

    Madupu R, Brinkac LM, Harrow J, Wilming LG, Böhme U, Lamesch P and Hannick LI

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

    PUBMED: 20428316; PMC: 2860899; DOI: 10.1093/database/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, Hancock RE and Harrow JL

    BMC genomics 2009;10;606

    PUBMED: 20003482; PMC: 2807441; DOI: 10.1186/1471-2164-10-606

Contact

Otterlace is maintained by the Anacode team at the Sanger Institute.

* quick link - http://q.sanger.ac.uk/9boxf8uw