DENOVOSEQ - GENE PREDICTION


Gene prediction is the methodology normally used to identify the regions of genomic DNA that encode genes (protein-coding and non-coding) as well as other regulatory regions and other functional elements. For eukaryotic genomes, we provide an interface within DeNovoSeq to run AUGUSTUS. For prokaryotic genes, we provide other solutions available in the SeqEditor app of the GPRO suite to extract ORFs from genomic sequences.


- Augustus: Augustus

Augustus (Stanke et al., 2008) predicts genes from eukaryotic genome sequences. Augustus can be used as an ab initio program (which means that the tool makes the prediction purely based on the sequence) The AUGUSTUS workflow implemented in DeNovoSeq is a step-to-step pipeline based three steps; “Training”, “Hints preparation” and “Prediction”. See the AUGUSTUS manual at http://bioinf.uni-greifswald.de/augustus/ for more information.

To fulfil the step of Training with DeNovoseq, go to:

            [ Gene prediction → Augustus → Training ]


Figure 23: Animated GIF of using a Gene Prediction Training application.

You will get a confirmation message that the job has been launched. Otherwise, revise all options again. If an input field is invalid or missing you will get an error icon beside the field (hover the mouse over it to see the error message).


Optional and if available, AUGUSTUS lets you to incorporate hints on the gene structure coming from extrinsic sources such as EST, protein alignments, RNAseq data, repeats. This is the step of Hints creation. If you have material to create the hints do as follows:


            [ Gene prediction → Augustus → Hints ]


Figure 24: Animated GIF of using a Gene Prediction Hints application.

If you already uploaded all material for creation of hints required for your gene prediction project, just click on the Run button to let Augustus create a GFF file per hint. At the end of the process DeNovoSeq will merged all hints into a single GFF

You will get a confirmation message that the job has been launched. Otherwise, revise all options again. If an input field is invalid or missing you will get an error icon beside the field (hover the mouse over it to see the error message).


Once you have the training already performed (and if you have the hints created), go to the final step Predictions and do the following:


            [ Gene prediction → Augustus → Prediction ]


Figure 25: Animated GIF of using a Gene Prediction Prediction application.

You will get a confirmation message that the job has been launched. Otherwise, revise all options again. If an input field is invalid or missing you will get an error icon beside the field (hover the mouse over it to see the error message).








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