Anacode and Annotools

Specialist analysis pipelines and annotation tools.

The 'Anacode' and 'Annotools' teams provide various graphical and command-line tools for use in genome annotation. Many of our tools can be used independently or in different combinations with each other to form different pipelines. They also use standard file formats to aid their integration into external pipelines.

[Genome Research Limited]

Tools

Annotation interfaces in Otterlace

Annotation interfaces in Otterlace

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  • Otterlace is an interactive, graphical client, which uses a local AceDB database with ZMap and perl/Tk tools to curate genomic annotation. Annotation is stored in an extended Ensembl schema (the "otter" database). The annotator is presented with a contiguous region of a chromosome to work on.
  • ZMap is a software package that provides a visualisation tool for genomic features. Written in C to give good display performance of large numbers of features it also provides a powerful programmatic interface allowing interaction with and modification of displayed features. Otterlace uses this interface to allow annotators to edit and display genome data stored in the Otter database.
  • Blixem is an interactive browser of pairwise alignments that have been stacked up in a "one-to-many" multiple alignment. It displays an overview section showing the positions of genes and alignments around the alignment window, and a detail section showing the actual alignment of protein or nucleotide sequences to the genomic DNA sequence. Blixem can be called from ZMap to view a set of alignments in more detail.
  • Dotter is a graphical dot-matrix program for detailed comparison of two sequences. Every residue in one sequence is compared to every residue in the other, with one sequence plotted on the x-axis and the other on the y-axis. Noise is filtered out so that alignments appear as diagonal lines. Dotter can be called from Blixem or Otterlace to analyse a particular alignment in greater detail.
  • Belvu is a multiple sequence alignment viewer and phylogenetic tool. It has an extensive set of user-configurable modes to color residues by conservation or by residue type, and some basic alignment editing capabilities. It can generate distance matrices between sequences and construct and view distance-based trees. It has many command-line options, making it suitable for use as part of a phylogenetic software pipeline. Belvu can also be called from Otterlace to view Pfam search results.
  • AceDB is a genome database designed specifically for handling bioinformatic data. It includes many programs and tools designed to manipulate and annotate genomic data and has been used in many projects across the world.

Availability

Packages

The tools are available in various different packages depending on which components you require:

  • The Otterlace annotation suite includes Otterlace, ZMap, Blixem, Dotter and Belvu.
  • The ZMap package contains the ZMap package.
  • The SeqTools package is a much smaller download containing just the alignment visualisation tools: Blixem, Dotter and Belvu.
  • The AceDB package includes tace, giface, xace, the acedb servers and many other tools.

Supported platforms

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

Licence

All of our tools are free software and are distributed under the terms of the GNU General Public License.

Users

The Otterlace annotation suite is used extensively by the HAVANA group for manual annotation. The Havana group is involved in the annotation genes as candidates for knockout in mouse for the Embryonic Stem (ES) Cell Mutagenesis team of Bill Skarnes as part of the EUCOMM and KOMP projects. Otterlace is also used remotely by KOMP annotators at the Genome Center at Washington University.

The AceDB database package as well as being used by otterlace is used extensively by other genome projects such as wormbase.

Belvu is used extensively by the Pfam group.

Contact

Bugs and feature requests

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

Anacode

The Anacode team (led by James Gilbert) develops the Otterlace analysis pipeline. The Anacode team also develops and maintains many of the software systems that support curation of reference genome sequences and WTSI sequence submission to the EMBL sequence database (the EBI partner of the INSDC database consortium).

For enquiries about any of these tools, email the Anacode team.

Annotools

The Annotools team (led by Ed Griffiths) develop the ZMap genome display engine, the SeqTools package (Blixem, Dotter and Belvu) and the AceDB package.

For enquiries about any of these tools, email the Annotools team.

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