You can select from each of the four (4) tools provide by PredHPI (Interolog, Domain-based, GOsim-PPIpred and Phylo-profiling), then you can either upload a multifasta file or paste your sequence(s) in the boxes, depending on the specific tool used you will have. When the result is ready you can download a file with that information to be open in a Spreadsheet (e.g: Excel) or visualize the proteins that were predicted as interacting, you can download your predicted network in Newick format. You can take a look of the step-by-step tutorial at Help.
| Module | Maximum number of Host sequences | Maximum number of Pathogen sequences |
|---|---|---|
| Interolog | 40,000 | 10,000 |
| Domain-based | 10,000 | 5,000 |
| GOsim | 2,000 | 1,000 |
| Phylo-profiling | 2,000 | 1,000 |
PredHPI has been thought to annotated intra-species and inter-species interactions from non-model organisms. However, our resources are limited so we encouraged our users to do a proper preparation of the queries that are large before submitting to avoid multiple submissions.
In that case you probably want to use each module separately and combine the results.
If you want fast results Interolog would be the best choice. Domain-based and Phylo-profiling have a similar performance as Interolog for small dataset. GOsim prediction is the slowest.
All independent resource databases or software used to implement PredHPI are named (and linked) in the tools pages by clicking the information buttons. A manuscript about this service is in progress in which all tools will be properly cited.
| Species name |
|---|
| Anopheles_gambiae |
| Arabidopsis_thaliana |
| Bos_taurus |
| Caenorhabditis_elegans |
| Canis_lupus_familiaris |
| Drosophila_melanogaster |
| Danio_rerio |
| Escherichia_coli |
| Gallus_gallus |
| Homo_sapiens |
| Mus_musculus |
| Macaca_mulatta |
| Plasmodium |
| Pan_troglodytes |
| Rattus_norvegicus |
| Saccharomyces_cerevisiae |
| Sus_scrofa |
| Xenopus_laevis |
UP82: It means Uniprot 82, which is the pool of genomes made from model uniprot proteomes.
| Species name |
|---|
| Absidia_glauca |
| Adelaide_River_virus |
| Apis_mellifera |
| Aquifex_aeolicus_strain_VF5 |
| Berne_virus |
| Bombyx_mori |
| Bos_taurus |
| Bovine_adenovirus |
| Brassica_napus |
| Breda_virus |
| Brome_mosaic_virus |
| Brucella_abortus_strain |
| Bunyamwera_virus |
| Canarypox_virus |
| Candida_auris |
| Capsicum_annuum |
| Cavia_porcellus |
| Chrysanthemum_virus_B |
| Columba_livia |
| Corchorus_capsularis |
| Cowpox_virus |
| Cucumis_melo |
| Ehrlichia_canis_strain_Jake |
| Escherichia_coli_strain_K12 |
| Eurypyga_helias |
| Folsomia_candida |
| Frankia_alni_strain_ACN14a |
| Galinsoga_mosaic_virus |
| Gallus_gallus |
| Glycine_soja |
| Gonium_pectorale |
| Hepatitis_delta_virus |
| Homo_sapiens |
| Isfahan_virus |
| Jatropha_curcas |
| JC_polyomavirus |
| Jembrana_disease_virus |
| Juglans_regia |
| Lagos_bat_virus |
| Lily_symptomless_virus |
| Mokola_virus |
| Musca_domestica |
| Mus_musculus |
| Myotis_brandtii |
| Naegleria_gruberi |
| Nestor_notabilis |
| Oikopleura_dioica |
| Orchesella_cincta |
| Oryctolagus_cuniculus |
| Ovis_aries |
| Pan_troglodytes |
| Papio_anubis |
| Phlebotomus_papatasi |
| Punica_granatum |
| Quercus_suber |
| Rattus_norvegicus |
| Rice_gall_dwarf_virus |
| Ricinus_communis |
| Rosa_chinensis |
| Salmo_salar |
| Schmallenberg_virus |
| Semliki_forest_virus |
| Shallot_virus_X |
| Sindbis_virus |
| Solanum_tuberosum |
| Southern_tomato_virus |
| Spinacia_oleracea |
| Stylonychia_lemnae |
| Sulcia_muelleri_strain_CARI |
| Sus_scrofa |
| Thermincola_potens_strain_JR |
| Toscana_virus |
| Trichuris_suis |
| Triticum_aestivum |
| Tupaia_paramyxovirus |
| Turnip_crinkle_virus |
| Tyto_alba |
| Vitis_vinifera |
| WU_polyomavirus |
| Zea_mays |
| Zika_virus |
| Zostera_marina |
If you can't get something to work or you want to suggest something to make this application works better, the developer would be happy to address any question at crissloaiza@gmail.com or cdloaiza@aggiemail.usu.edu.