gene_prediction_just_augustus
This is an old revision of the document!
By Jason Shao (Last Edited: October 25th 2024)
Intro
Augustus is an ab initio gene predictor that employs Hidden Markov Models (HMMs) pre-trained on existing datasets. Training a custom HMM model with your own data is possible, but in this basic tutorial, we are only going to use a pre-existing model.
Example Usage
augustus \
--species=generic \
<your genome> \
--gff3=on \
--outfile=<outfile name>.gff3
Note that the species here is set to generic to minimize biases for a divergent organism. If your organism is closely related to one of the pre-trained species below, you can specify that instead to yield a better prediction.
| Identifier | Species | Major Lineage |
|---|---|---|
| human | Homo sapiens | Opisthokonta (Metazoa) |
| fly | Drosophila melanogaster | Opisthokonta (Metazoa) |
| arabidopsis | Arabidopsis thaliana | Archaeplastida (Plantae) |
| brugia | Brugia malayi | Opisthokonta (Metazoa) |
| aedes | Aedes aegypti | Opisthokonta (Metazoa) |
| tribolium | Tribolium castaneum | Opisthokonta (Metazoa) |
| schistosoma | Schistosoma mansoni | Opisthokonta (Metazoa) |
| tetrahymena | Tetrahymena thermophila | SAR (Alveolata) |
| galdieria | Galdieria sulphuraria | Archaeplastida (Plantae) |
| maize | Zea mays | Archaeplastida (Plantae) |
| toxoplasma | Toxoplasma gondii | SAR (Alveolata) |
| caenorhabditis | Caenorhabditis elegans | Opisthokonta (Metazoa) |
| aspergillus_fumigatus | Aspergillus fumigatus | Opisthokonta (Fungi) |
| aspergillus_nidulans | Aspergillus nidulans | Opisthokonta (Fungi) |
| aspergillus_oryzae | Aspergillus oryzae | Opisthokonta (Fungi) |
| aspergillus_terreus | Aspergillus terreus | Opisthokonta (Fungi) |
| botrytis_cinerea | Botrytis cinerea | Opisthokonta (Fungi) |
| candida_albicans | Candida albicans | Opisthokonta (Fungi) |
| candida_guilliermondii | Candida guilliermondii | Opisthokonta (Fungi) |
| candida_tropicalis | Candida tropicalis | Opisthokonta (Fungi) |
| chaetomium_globosum | Chaetomium globosum | Opisthokonta (Fungi) |
| coccidioides_immitis | Coccidioides immitis | Opisthokonta (Fungi) |
| coprinus | Coprinus cinereus | Opisthokonta (Fungi) |
| coyote_tobacco | Nicotiana attenuata | Archaeplastida (Plantae) |
| cryptococcus_neoformans_gattii | Cryptococcus neoformans gattii | Opisthokonta (Fungi) |
| cryptococcus_neoformans_neoformans_B | Cryptococcus neoformans | Opisthokonta (Fungi) |
| debaryomyces_hansenii | Debaryomyces hansenii | Opisthokonta (Fungi) |
| encephalitozoon_cuniculi_GB | Encephalitozoon cuniculi | Opisthokonta (Fungi) |
| eremothecium_gossypii | Eremothecium gossypii | Opisthokonta (Fungi) |
| fusarium_graminearum | Fusarium graminearum | Opisthokonta (Fungi) |
| histoplasma_capsulatum | Histoplasma capsulatum | Opisthokonta (Fungi) |
| kluyveromyces_lactis | Kluyveromyces lactis | Opisthokonta (Fungi) |
| laccaria_bicolor | Laccaria bicolor | Opisthokonta (Fungi) |
| lamprey | Petromyzon marinus | Opisthokonta (Metazoa) |
| leishmania_tarentolae | Leishmania tarentolae | Excavata |
| lodderomyces_elongisporus | Lodderomyces elongisporus | Opisthokonta (Fungi) |
| magnaporthe_grisea | Magnaporthe grisea | Opisthokonta (Fungi) |
| neurospora_crassa | Neurospora crassa | Opisthokonta (Fungi) |
| phanerochaete_chrysosporium | Phanerochaete chrysosporium | Opisthokonta (Fungi) |
| pichia_stipitis | Pichia stipitis | Opisthokonta (Fungi) |
| rhizopus_oryzae | Rhizopus oryzae | Opisthokonta (Fungi) |
| saccharomyces_cerevisiae_S288C | Saccharomyces cerevisiae | Opisthokonta (Fungi) |
| schizosaccharomyces_pombe | Schizosaccharomyces pombe | Opisthokonta (Fungi) |
| thermoanaerobacter_tengcongensis | Thermoanaerobacter tengcongensis | Bacteria |
| trichinella | Trichinella spiralis | Opisthokonta (Metazoa) |
| ustilago_maydis | Ustilago maydis | Opisthokonta (Fungi) |
| yarrowia_lipolytica | Yarrowia lipolytica | Opisthokonta (Fungi) |
| nasonia | Nasonia vitripennis | Opisthokonta (Metazoa) |
| tomato | Solanum lycopersicum | Archaeplastida (Plantae) |
| chlamydomonas | Chlamydomonas reinhardtii | Archaeplastida |
| amphimedon | Amphimedon queenslandica | Opisthokonta (Metazoa) |
| pneumocystis | Pneumocystis jirovecii | Opisthokonta (Fungi) |
| wheat | Triticum aestivum | Archaeplastida (Plantae) |
| chicken | Gallus gallus | Opisthokonta (Metazoa) |
| zebrafish | Danio rerio | Opisthokonta (Metazoa) |
| E_coli_K12 | Escherichia coli | Bacteria |
| s_aureus | Staphylococcus aureus | Bacteria |
| volvox | Volvox carteri | Archaeplastida |
gene_prediction_just_augustus.1729884138.txt.gz · Last modified: by 134.190.221.230