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Gene Prediction with AUGUSTUS in comparative gene prediction (cgp) mode

genes are predicted simultaneously in several aligned genomes

INTRODUCTION
INSTALLATION
RUNNING AUGUSTUS IN CGP MODE
BUILDING THE NEWICK PARSER FROM SCRATCH
(not needed unless you run into compiler errors related to ‘parse.cc’ or ‘lex.cc’)
AUTHORS AND CONTACT
REFERENCES
LICENSES

INTRODUCTION

The cgp mode is an extension to AUGUSTUS that takes an alignment of two or more genomes and simultaneously predicts genes in all of them. Beside the genomes and the alignment, a phylogenetic tree of the species is required input. AUGUSTUS-cgp can either be used

Both genomes and extrinsic evidence can either be read in from a flat file or alternatively retrieved from a MySQL or SQLite database.
All three approaches are described below in more detail.

This manual assumes that you are already familiar with AUGUSTUS and that you know how to use AUGUSTUS for gene prediction in a single genome.

INSTALLATION

Install dependencies

See these instructions for a complete overview.

Enable cgp mode

Open the file common.mk with a text editor and uncomment the following lines to enable comparative gene prediction.

COMPGENEPRED = true

To support a SQLite database uncomment this line

 SQLite = true

or for MySQL this

 MYSQL = true

Compile from sources

Once all dependencies are available, you can compile AUGUSTUS using make.

make

In case you had previously compiled AUGUSTUS with disabled cgp mode first you have to call

make clean

After compilation has finished, the command bin/augustus should be executable and print a usage message.