PredGenesGetPepts

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

General information and applicability

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.

Installation

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/PredGenesGetPepts

Secondly, run :

cd PredGenesGetPepts
bash setup.sh

Everything should now be set up and ready to run, test the installation by executing:

source ~/.bash_aliases
pregegepep -h

Alternatively, 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 -h

Options and testing

You 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 message

To 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 5

You will get the same results you can find in predgengetpepts_results_test folder.

Supported species

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

License and rights of usage

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.

References

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