Configuring and Using the
Apollo Genome Browser with Mogul
The Apollo genome browser is Java-based software tool jointly developed between the Berkeley Drosophila Genome Project, USA and the Sanger Institute, Cambridge, UK. Whilst the browser is primarily designed for viewing and editing gene-orientated annotation, it is also an excellent tool for visualising motif predictions.
Mogul specifically generates motif predictions in GFF format and it is Apollo's capabilites to upload and display such a format that is exploited.
Apollo can be downloaded from the Berkeley Drosophila website. It is available for all major software platforms and installs via an InstallAnywhere tool.
Apollo can be downloaded from: http://www.fruitfly.org/annot/apollo
Apollo is highly user-configurable via a set of configuration files. This allows user specific annotation tracks to be added to the Apollo display where, for example, the colour, scaling and labelling of features can be customised. To optimally display motif predictions from the variety of algorithms employed by Mogul, some simple configuration changes are required to the default configuration of Apollo.
Apollo can be configured as follows:
Change to the directory where you installed Apollo.
Change to the conf directory.
Download the mogul.tiers into this directory. This file contains the colour and scaling attributes for the motif predictions.
Edit the file gff.style. For the line beginning with Types, replace “ensembl.tiers” with “mogul.tiers". This causes Apollo to upload the Mogul specific parameters when it starts up.
Edit the file apollo.cfg. For the line that starts SiteShowLimit, change the default value from 15 to 0. This switches off the option to display stop/start codons, which can be confusing when looking at motif predictions.
To display motif predictions using Apollo you need both a GFF results file and a file in FASTA format containing the DNA sequence.
After starting your copy of Apollo, from the 'Choose data adapter' menu, select the option 'Ensembl GFF file format'. Use the Browse buttons to upload the relevant GFF and FASTA. Click Ok to launch the viewing panel.
Prepared using OpenOffice 1.0.1
Apollo Configuration: 6th May 2004 Ver.1.0