Difference between revisions of "Augustus"
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|{{#vardefine:url|http://augustus.gobics.de/}} | |{{#vardefine:url|http://augustus.gobics.de/}} | ||
<!--CONFIGURATION: OPTIONAL (1=ON)--> | <!--CONFIGURATION: OPTIONAL (1=ON)--> | ||
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|{{#vardefine:exe|}} <!--RUNNING --> | |{{#vardefine:exe|}} <!--RUNNING --> | ||
|{{#vardefine:conf|}} <!--CONFIGS--> | |{{#vardefine:conf|}} <!--CONFIGS--> | ||
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mechanism for incorporating extrinsic information, e.g. from EST alignments | mechanism for incorporating extrinsic information, e.g. from EST alignments | ||
and protein alignments. | and protein alignments. | ||
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<!--Modules--> | <!--Modules--> | ||
==Required Modules== | ==Required Modules== | ||
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===Serial=== | ===Serial=== | ||
*{{#var:app}} | *{{#var:app}} | ||
| − | + | ==System Variables== | |
| + | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
Revision as of 17:20, 10 August 2012
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
Serial
- augustus
System Variables
- HPC_{{#uppercase:augustus}}_DIR - installation directory