AUGUSTUS gene prediction using Zebrafish data as a reference specie.

Question

[Shin Taguchi]

Hi.

I would like to use AUGUSTUS to predict the genes of a certain fish.

On the AUGUSTUS website, the list of species that can be used as references for gene prediction includes zebrafish, but zebrafish is not included in the list output when the following command is executed.

augustus --species=help

identifier                               | species
-----------------------------------------|----------------------
human                                    | Homo sapiens
fly                                      | Drosophila melanogaster
arabidopsis                              | Arabidopsis thaliana
brugia                                   | Brugia malayi
aedes                                    | Aedes aegypti
tribolium                                | Tribolium castaneum
schistosoma                              | Schistosoma mansoni
tetrahymena                              | Tetrahymena thermophila
galdieria                                | Galdieria sulphuraria
maize                                    | Zea mays
toxoplasma                               | Toxoplasma gondii
caenorhabditis                           | Caenorhabditis elegans
(elegans)                                | Caenorhabditis elegans
aspergillus_fumigatus                    | Aspergillus fumigatus
aspergillus_nidulans                     | Aspergillus nidulans
(anidulans)                              | Aspergillus nidulans
aspergillus_oryzae                       | Aspergillus oryzae
aspergillus_terreus                      | Aspergillus terreus
botrytis_cinerea                         | Botrytis cinerea
candida_albicans                         | Candida albicans
candida_guilliermondii                   | Candida guilliermondii
candida_tropicalis                       | Candida tropicalis
chaetomium_globosum                      | Chaetomium globosum
coccidioides_immitis                     | Coccidioides immitis
coprinus                                 | Coprinus cinereus
coprinus_cinereus                        | Coprinus cinereus
cryptococcus_neoformans_gattii           | Cryptococcus neoformans gattii
cryptococcus_neoformans_neoformans_B     | Cryptococcus neoformans neoformans
cryptococcus_neoformans_neoformans_JEC21 | Cryptococcus neoformans neoformans
(cryptococcus)                           | Cryptococcus neoformans
debaryomyces_hansenii                    | Debaryomyces hansenii
encephalitozoon_cuniculi_GB              | Encephalitozoon cuniculi
eremothecium_gossypii                    | Eremothecium gossypii
fusarium_graminearum                     | Fusarium graminearum
(fusarium)                               | Fusarium graminearium
histoplasma_capsulatum                   | Histoplasma capsulatum
(histoplasma)                            | Histoplasma capsulatum
kluyveromyces_lactis                     | Kluyveromyces lactis
laccaria_bicolor                         | Laccaria bicolor
lodderomyces_elongisporus                | Lodderomyces elongisporus
magnaporthe_grisea                       | Magnaporthe grisea
neurospora_crassa                        | Neurospora crassa
(neurospora)                             | Neurospora crassa
phanerochaete_chrysosporium              | Phanerochaete chrysosporium
(pchrysosporium)                         | Phanerochaete chrysosporium
pichia_stipitis                          | Pichia stipitis
rhizopus_oryzae                          | Rhizopus oryzae
saccharomyces_cerevisiae_S288C           | Saccharomyces cerevisiae
saccharomyces_cerevisiae_rm11-1a_1       | Saccharomyces cerevisiae
(saccharomyces)                          | Saccharomyces cerevisiae
schizosaccharomyces_pombe                | Schizosaccharomyces pombe
ustilago_maydis                          | Ustilago maydis
(ustilago)                               | Ustilago maydis
yarrowia_lipolytica                      | Yarrowia lipolytica
nasonia                                  | Nasonia vitripennis
tomato                                   | Solanum lycopersicum
chlamydomonas                            | Chlamydomonas reinhardtii
amphimedon                               | Amphimedon queenslandica
pea_aphid                                | Acyrthosiphon pisum

Is it possible to use zebrafish as a reference species when making gene predictions with AUGUSTUS?

[Juke34]

What Augustus version are you using?

[Shin Taguchi]

Juke34

I was using version 3.2.2, but when I used version 3.4.0, I saw zebrafish in the species list. Thank you very much!