PredGenesGetPepts is an easy-to-use, beginner-friendly pipeline to call genes from fasta files, retrieve peptides from it and blasting them against a given protein database
PredGenesGetPepts was designed as a gene-calling and peptide identification tool: a fasta file containing the to-be-investigated genetic region(s), a protein database and a taxonomic unit (at least orientative) are thus needed for the analysis.
For the gene-calling portion, PredGenesGetPepts is based on Augustus (version 3.4.0): this comes with the advantages of its easy-to-read output and quickness, but puts also a limitation on the applicability of the pipeline, as Augustus can identify genes from a limited number of species (see Supported species for more).
Gene calling output is a gff3 file, which is placed within the same folder of the original fasta file, located in a specifically generated directory named predgengetpepts_results.
After that, the python script readaugustus.py reads the gff3 output from Augustus and extract the protein sequence(s): after that, it prints them to a .faa file placed within the predgengetpepts_results folder.
The last step involves BLASTing, which is performed against the user-specified database: it returns a txt file that encompasses results from BLAST in tabular format.
The basic requirment for this installation is to have Mamba and Conda up and running on your Linux machine. If you don't match this pre-requisite, consider downloading them from the dedicated pages.
To install PredGenesGetPepts, first of all run:
git init
git clone https://github.com/AstraBert/PredGenesGetPeptsSecondly, run :
cd PredGenesGetPepts
bash setup.shEverything should now be set up and ready to run, test the installation by executing:
source ~/.bash_aliases
pregegepep -hAlternatively, you can download the code from the Realeases page:
- Download the PredGenesGetPepts.tar.gz archive file
- Move to the directory were you stored the downloaded file
- Run:
tar -xzvf ./PredGenesGetPepts.tar.gz- You will now have the complete directory; run:
cd PredGenesGetPepts
bash setup.sh
source ~/.bash_aliases
pregegepep -hYou will have to use the following options to correctly exploit PredGenGetPepts:
Usage: pregegepep -i,--infile INFILE -db, --database DATABASE -s,--species SPECIES
REQUIRED ARGUMENTS:
-i, --infile: Provide the path to the original fasta file from which to start the phylogenetic analysis
-db, --database: Provide the path to the database against with blastp will be conducted
-s,--species: Provide the identifier of the (expected) species you are calling genes against (needed for Augustus)
OPTIONAL ARGUMENTS:
-max, --max_target_seqs: Provide the maximum number of hits you want blast to return (default is 100)
Input pregegepep -h,--help to show this messageTo test the program, execute the following code (that assumes you have already moved to the PredGenGetPepts directory):
conda activate ./environments/predgenesgetpepts
cd ./test
makeblastdb -in ./proteins.faa -out ./proteinsDB -dbtype prot
conda deactivate
pregegepep -i ./test.fasta -db ./proteinsDB -s human -max 5You will get the same results you can find in predgengetpepts_results_test folder.
Up to the employed version of Augustus, there are 108 species that can be gene-called, which are the following:
| Identifier | Species |
|---|---|
| pea_aphid | Acyrthosiphon pisum |
| aedes | Aedes aegypti |
| amphimedon | Amphimedon queenslandica |
| ancylostoma_ceylanicum | Ancylostoma ceylanicum |
| adorsata | Apis dorsata |
| honeybee1 | Apis mellifera |
| arabidopsis | Arabidopsis thaliana |
| aspergillus_fumigatus | Aspergillus fumigatus |
| aspergillus_nidulans | Aspergillus nidulans |
| (anidulans) | Aspergillus nidulans |
| aspergillus_oryzae | Aspergillus oryzae |
| aspergillus_terreus | Aspergillus terreus |
| bombus_impatiens1 | Bombus impatiens |
| bombus_terrestris2 | Bombus terrestris |
| botrytis_cinerea | Botrytis cinerea |
| brugia | Brugia malayi |
| b_pseudomallei | Burkholderia pseudomallei |
| caenorhabditis | Caenorhabditis elegans |
| (c_elegans_trsk) | Caenorhabditis elegans |
| (elegans) | Caenorhabditis elegans |
| elephant_shark | Callorhinchus milii |
| camponotus_floridanus | Camponotus floridanus |
| candida_albicans | Candida albicans |
| candida_guilliermondii | Candida guilliermondii |
| candida_tropicalis | Candida tropicalis |
| chaetomium_globosum | Chaetomium globosum |
| chiloscyllium | Chiloscyllium punctatum |
| chlamy2011 | Chlamydomonas reinhardtii |
| (chlamydomonas) | Chlamydomonas reinhardtii |
| chlorella | Chlorella sp. |
| ciona | Ciona intestinalis |
| coccidioides_immitis | Coccidioides immitis |
| coccidioides_immitis | Coccidioides immitis |
| Conidiobolus_coronatus | Conidiobolus coronatus |
| coprinus_cinereus | Coprinus cinereus |
| coprinus_cinereus | Coprinus cinereus |
| (coprinus) | Coprinus cinereus |
| coprinus | Coprinus cinereus |
| cryptococcus_neoformans_gattii | Cryptococcus neoformans gattii |
| cryptococcus_neoformans_neoformans_B | Cryptococcus neoformans neoformans |
| (cryptococcus) | Cryptococcus neoformans |
| culex | Culex pipiens |
| zebrafish | Danio rerio |
| debaryomyces_hansenii | Debaryomyces hansenii |
| fly | Drosophila melanogaster |
| (fly_exp) | Drosophila melanogaster |
| encephalitozoon_cuniculi_GB | Encephalitozoon cuniculi |
| eremothecium_gossypii | Eremothecium gossypii |
| E_coli_K12 | Escherichia coli K12 |
| fusarium_graminearum | Fusarium graminearium |
| (fusarium) | Fusarium graminearium |
| galdieria | Galdieria sulphuraria |
| chicken | Gallus gallus domesticus |
| heliconius_melpomene1 | Heliconius melpomene |
| histoplasma_capsulatum | Histoplasma capsulatum |
| (histoplasma) | Histoplasma capsulatum |
| human | Homo sapiens |
| kluyveromyces_lactis | Kluyveromyces lactis |
| laccaria_bicolor | Laccaria bicolor |
| leishmania_tarentolae | Leishmania tarentolae |
| japaneselamprey | Lethenteron camtschaticum |
| lodderomyces_elongisporus | Lodderomyces elongisporus |
| magnaporthe_grisea | Magnaporthe grisea |
| mnemiopsis_leidyi | Mnemiopsis leidyi |
| nasonia | Nasonia vitripennis |
| nematostella_vectensis | Nematostella vectensis |
| neurospora_crassa | Neurospora crassa |
| (neurospora) | Neurospora crassa |
| coyote_tobacco | Nicotiana attenuata |
| rice | Oryza sativa |
| parasteatoda | Parasteatoda sp. |
| sealamprey | Petromyzon marinus |
| phanerochaete_chrysosporium | Phanerochaete chrysosporium |
| (pchrysosporium) | Phanerochaete chrysosporium |
| pichia_stipitis | Pichia stipitis |
| pisaster | Pisaster ochraceus |
| pfalciparum | Plasmodium falciparum |
| pneumocystis | Pneumocystis jirovecii |
| rhincodon | Rhincodon typus |
| rhizopus_oryzae | Rhizopus oryzae |
| rhodnius | Rhodnius prolixus |
| saccharomyces_cerevisiae_rm11-1a_1 | Saccharomyces cerevisiae |
| saccharomyces_cerevisiae_S288C | Saccharomyces cerevisiae |
| (saccharomyces) | Saccharomyces cerevisiae |
| schistosoma | Schistosoma mansoni |
| (schistosoma2) | Schistosoma mansoni |
| schizosaccharomyces_pombe | Schizosaccharomyces pombe |
| scyliorhinus | Scyliorhinus torazame |
| tomato | Solanum lycopersicum |
| s_aureus | Staphylococcus aureus |
| s_pneumoniae | Streptococcus pneumoniae |
| strongylocentrotus_purpuratus | Strongylocentrotus purpuratus |
| sulfolobus_solfataricus | Sulfolobus solfataricus |
| tetrahymena | Tetrahymena thermophila |
| cacao | Theobroma cacao |
| thermoanaerobacter_tengcongensis | Thermoanaerobacter tengcongensis |
| toxoplasma | Toxoplasma gondii |
| tribolium2012 | Tribolium castaneum |
| trichinella | Trichinella sp. |
| wheat | Triticum sp. |
| ustilago_maydis | Ustilago maydis |
| (ustilago) | Ustilago maydis |
| verticillium_albo_atrum1 | Verticillium albo atrum |
| verticillium_longisporum1 | Verticillium longisporum |
| volvox | Volvox sp. |
| Xipophorus_maculatus | Xipophorus maculatus |
| yarrowia_lipolytica | Yarrowia lipolytica |
| maize | Zea mays |
| (maize5) | Zea mays |
The code is protected by the GNU v.3 license. As the license provider reports: "Permissions of this strong copyleft license are conditioned on making available complete source code of licensed works and modifications, which include larger works using a licensed work, under the same license. Copyright and license notices must be preserved. Contributors provide an express grant of patent rights".
Please note that PredGenGetPepts is still experimental and may contain errors, may fail/take really long while performing large analyses with limited computational power (e.g. on a normal laptop) and may output not-100%-reliable results, so always check them and pull issues whenever you feel it to be the case, we'll be on your back as soon as possible to fix/implement/enhance whatever you suggest!
If you are using PredGenGetPepts for you project, please consider to cite the author of this code (Astra Bertelli) and this GitHub repository.
augustus: Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011) A novel hybrid gene prediction method employing protein multiple sequence alignments Bioinformatics, doi: 10.1093/bioinformatics/btr010
blast: Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and applications. BMC bioinformatics, 10, 421. https://doi.org/10.1186/1471-2105-10-421