Difference between revisions of "Augustus"

Revision as of 22:16, 25 January 2017

Description

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server or be downloaded and run locally. AUGUSTUS usually belongs to the most accurate programs for the species it is trained for. Often it is the most accurate ab initio program. AUGUSTUS can predict alternative splicing and alternative transcripts. AUGUSTUS can predict the 5'UTR and 3'UTR including introns. AUGUSTUS is retrainable. It comes with a training program that estimates the parameters given a training set of known genes. It also comes with an optimization script that tries to find values for the meta parameters, like splice window sizes, that optimize the prediction accuracy. AUGUSTUS can be used ab initio and has a flexible mechanism for incorporating extrinsic information, e.g. from EST alignments and protein alignments.

Required Modules

modules documentation

Serial

augustus

System Variables

HPC_{{#uppercase:augustus}}_DIR - installation directory

Additional Information

Since the directory where Augustus is installed is now user-writable set the '$AUGUSTUS_CONFIG_PATH' variable to a path in your scratch space e.g.

export AUGUSTUS_CONFIG_PATH=/ufrc/group/user/some/project/augustus_conf_dir

@@ Line 4: / Line 4: @@
 |{{#vardefine:url|http://augustus.gobics.de/}}
 <!--CONFIGURATION: OPTIONAL (1=ON)-->
-|{{#vardefine:exe|}} <!--RUNNING -->
+|{{#vardefine:exe|1}} <!--RUNNING -->
 |{{#vardefine:conf|}} <!--CONFIGS-->
 |{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
@@ Line 39: / Line 39: @@
 <!--Additional-->
 {{#if: {{#var: exe}}|==Additional Information==
-DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY
+Since the directory where Augustus is installed is now user-writable set the '<code>$AUGUSTUS_CONFIG_PATH</code>' variable to a path in your scratch space e.g.
+ export AUGUSTUS_CONFIG_PATH=/ufrc/group/user/some/project/augustus_conf_dir
 |}}
 <!--Configuration-->