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AUGUSTUS can report a large number of alternative genes, including probabilities for the transcripts and each exon and intron. You can make AUGUSTUS predict suboptimal gene structures (example) and you can adjust command line paramters to regulate the number of reported alternatives.
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. Augustus [gene prediction] University of Göttingen - Faculty of Biology - Institute of Microbiology and Genetics - Department of Bioinformatics
AUGUSTUS is a program to find genes and their structures in one or more genomes. More ... Windows users can use the Windows Subsystem for Linux (WSL) to install AUGUSTUS exactly as described below for Linux. How to set up the WSL for AUGUSTUS is described here.
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run with pre-trained parameters on this web server or be downloaded and run locally. It is open source so you can compile it for your computing platform. You can also run AUGUSTUS on the German MediGRID.
This website explains step-by-step how to use the AUGUSTUS prediction web server application to predict genes in a genomic sequence. You find a similar tutorial on how to train AUGUSTUS parameters here (click). Functionalities of the AUGUSTUS prediction web server application are (with a single run):
PREDICT GENES AB INITIO</h2> <i>Ab initio</i> prediction means that no other input is used than the target genome itself. Below, you will find examples of predictions that use evidence (hints), here we use none. <span class="assignment">Predict the genes in the range 7,000,001-7,500,000 of chr2R of <i>D. melanogaster</i></span>.
AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and syntenic genomic alignments. Since version 3.0 AUGUSTUS can also predict the genes simultaneously in several aligned genomes (see README-cgp.md ).
AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and syntenic genomic alignments. Since version 3.0 AUGUSTUS can also predict the genes simultaneously in several aligned genomes (see README-cgp.md ).
Predict the genes in the range 7,000,001-7,500,000 of chr2R of D. melanogaster. Use the FASTA format file chr2R.fa, which includes the whole chromosome 2R. To shorten this test run (or when running several jobs in parallel) you should specify a subrange of the input sequence using the parameters --predictionStart and --predictionEnd.
May 21, 2013 · AUGUSTUS is one of the most accurate tools for eukaryotic gene prediction. Here, we present WebAUGUSTUS, a web interface for training AUGUSTUS and predicting genes with AUGUSTUS. Depending on the needs of the user, WebAUGUSTUS generates training gene structures automatically.
