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faq.html
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<!DOCTYPE html>
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<a href="http://bioinfo.usu.edu" target="_blank" ><h6 style="font-size: 14px;">Kaundal Bioinformatics Laboratory</h6></a>
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<h1 class="display-4" align="Center"> Frequently Asked Questions (FAQ)</h1>
<div class="col-md-12" >
<div class="card-box" style="font-size: 18px;margin-top: 30px;">
<button type="button" id="howsubmitH" class="btn btn-large btn-light waves-effect" data-toggle="collapse" data-target="#howsubmitB">How to Submit a Job in PredHPI <span class="btn-label btn-label-right" style="z-index: 0;"> <i class="fa fa-arrow-down"></i></span> </button>
<div id="howsubmitB" class="collapse" style="font-size: 18px;">
<p> 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 <a href="help.html">Help</a>.</p>
</div>
<br>
<br>
<button type="button" id="maxseqH" class="btn btn-large btn-light waves-effect" data-toggle="collapse" data-target="#maxseqB" style="z-index: 0;">Maximum number of sequences <span class="btn-label btn-label-right"> <i class="fa fa-arrow-down"></i></span></button>
<div id="maxseqB" class="collapse" style="font-size: 18px;">
<table class="table table-bordered">
<thead>
<tr>
<th>Module</th>
<th>Maximum number of Host sequences</th>
<th>Maximum number of Pathogen sequences</th>
</tr>
</thead>
<tbody>
<tr>
<td>Interolog</td>
<td>40,000</td>
<td>10,000</td>
</tr>
<tr>
<td>Domain-based</td>
<td>10,000</td>
<td>5,000</td>
</tr>
<tr>
<td>GOsim</td>
<td>2,000</td>
<td>1,000</td>
</tr>
<tr>
<td>Phylo-profiling</td>
<td>2,000</td>
<td>1,000</td>
</tr>
</tbody>
</table>
<p>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.</p>
</div>
<br>
<br>
<button type="button" id="bannotH" class="btn btn-large btn-light waves-effect" data-toggle="collapse" data-target="#bannotB" style="z-index: 0;">Which tool should I use if I want the best annotation<span class="btn-label btn-label-right"> <i class="fa fa-arrow-down"></i></span></button>
<div id="bannotB" class="collapse" style="font-size: 18px;">
<p>In that case you probably want to use each module separately and combine the results.</p>
</div>
<br>
<br>
<button type="button" id="fannotH" class="btn btn-large btn-light waves-effect" data-toggle="collapse" data-target="#fannotB" style="z-index: 0;">Which tool should I use if I want the fastest annotation<span class="btn-label btn-label-right"> <i class="fa fa-arrow-down"></i></span></button>
<div id="fannotB" class="collapse" style="font-size: 18px;">
<p>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.</p>
</div>
<br>
<br>
<button type="button" id="thirdsH" class="btn btn-large btn-light waves-effect" data-toggle="collapse" data-target="#thirdsB" style="z-index: 0;">Which third party software and resources do you use in the service <span class="btn-label btn-label-right"> <i class="fa fa-arrow-down"></i></span></button>
<div id="thirdsB" class="collapse" style="font-size: 18px;">
<p>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.</p>
</div>
<br>
<br>
<button type="button" id="poolsH" class="btn btn-large btn-light waves-effect" data-toggle="collapse" data-target="#poolsB" style="z-index: 0;">In Phylo-Profiling, what UP82 and BC18 means<span class="btn-label btn-label-right"> <i class="fa fa-arrow-down"></i></span> </button>
<div id="poolsB" class="collapse" style="font-size: 18px;">
<b>BC18</b>: It means Bioconductor 18, which is the pool of genomes made from the 18 Bioconductor Org.DB species annotated.</p>
<div class="col-sm-8">
<table class="table table-bordered" style="font-size: 16px">
<thead>
<tr>
<th>Species name</th>
</tr>
</thead>
<tbody>
<tr>
<td>Anopheles_gambiae</td>
</tr>
<tr>
<td>Arabidopsis_thaliana</td>
</tr>
<tr>
<td>Bos_taurus</td>
</tr>
<tr>
<td>Caenorhabditis_elegans</td>
</tr>
<tr>
<td>Canis_lupus_familiaris</td>
</tr>
<tr>
<td>Drosophila_melanogaster</td>
</tr>
<tr>
<td>Danio_rerio</td>
</tr>
<tr>
<td>Escherichia_coli</td>
</tr>
<tr>
<td>Gallus_gallus</td>
</tr>
<tr>
<td>Homo_sapiens</td>
</tr>
<tr>
<td>Mus_musculus</td>
</tr>
<tr>
<td>Macaca_mulatta</td>
</tr>
<tr>
<td>Plasmodium</td>
</tr>
<tr>
<td>Pan_troglodytes</td>
</tr>
<tr>
<td>Rattus_norvegicus</td>
</tr>
<tr>
<td>Saccharomyces_cerevisiae</td>
</tr>
<tr>
<td>Sus_scrofa</td>
</tr>
<tr>
<td>Xenopus_laevis</td>
</tr>
</tbody>
</table>
</div>
<p><b>UP82</b>: It means Uniprot 82, which is the pool of genomes made from model uniprot proteomes.</p>
<div class="col-sm-8">
<table class="table table-bordered" style="font-size: 16px">
<thead>
<tr>
<th>Species name</th>
</tr>
</thead>
<tbody>
<tr>
<td>Absidia_glauca</td>
</tr>
<tr>
<td>Adelaide_River_virus</td>
</tr>
<tr>
<td>Apis_mellifera</td>
</tr>
<tr>
<td>Aquifex_aeolicus_strain_VF5</td>
</tr>
<tr>
<td>Berne_virus</td>
</tr>
<tr>
<td>Bombyx_mori</td>
</tr>
<tr>
<td>Bos_taurus</td>
</tr>
<tr>
<td>Bovine_adenovirus</td>
</tr>
<tr>
<td>Brassica_napus</td>
</tr>
<tr>
<td>Breda_virus</td>
</tr>
<tr>
<td>Brome_mosaic_virus</td>
</tr>
<tr>
<td>Brucella_abortus_strain</td>
</tr>
<tr>
<td>Bunyamwera_virus</td>
</tr>
<tr>
<td>Canarypox_virus</td>
</tr>
<tr>
<td>Candida_auris</td>
</tr>
<tr>
<td>Capsicum_annuum</td>
</tr>
<tr>
<td>Cavia_porcellus</td>
</tr>
<tr>
<td>Chrysanthemum_virus_B</td>
</tr>
<tr>
<td>Columba_livia</td>
</tr>
<tr>
<td>Corchorus_capsularis</td>
</tr>
<tr>
<td>Cowpox_virus</td>
</tr>
<tr>
<td>Cucumis_melo</td>
</tr>
<tr>
<td>Ehrlichia_canis_strain_Jake</td>
</tr>
<tr>
<td>Escherichia_coli_strain_K12</td>
</tr>
<tr>
<td>Eurypyga_helias</td>
</tr>
<tr>
<td>Folsomia_candida</td>
</tr>
<tr>
<td>Frankia_alni_strain_ACN14a</td>
</tr>
<tr>
<td>Galinsoga_mosaic_virus</td>
</tr>
<tr>
<td>Gallus_gallus</td>
</tr>
<tr>
<td>Glycine_soja</td>
</tr>
<tr>
<td>Gonium_pectorale</td>
</tr>
<tr>
<td>Hepatitis_delta_virus</td>
</tr>
<tr>
<td>Homo_sapiens</td>
</tr>
<tr>
<td>Isfahan_virus</td>
</tr>
<tr>
<td>Jatropha_curcas</td>
</tr>
<tr>
<td>JC_polyomavirus</td>
</tr>
<tr>
<td>Jembrana_disease_virus</td>
</tr>
<tr>
<td>Juglans_regia</td>
</tr>
<tr>
<td>Lagos_bat_virus</td>
</tr>
<tr>
<td>Lily_symptomless_virus</td>
</tr>
<tr>
<td>Mokola_virus</td>
</tr>
<tr>
<td>Musca_domestica</td>
</tr>
<tr>
<td>Mus_musculus</td>
</tr>
<tr>
<td>Myotis_brandtii</td>
</tr>
<tr>
<td>Naegleria_gruberi</td>
</tr>
<tr>
<td>Nestor_notabilis</td>
</tr>
<tr>
<td>Oikopleura_dioica</td>
</tr>
<tr>
<td>Orchesella_cincta</td>
</tr>
<tr>
<td>Oryctolagus_cuniculus</td>
</tr>
<tr>
<td>Ovis_aries</td>
</tr>
<tr>
<td>Pan_troglodytes</td>
</tr>
<tr>
<td>Papio_anubis</td>
</tr>
<tr>
<td>Phlebotomus_papatasi</td>
</tr>
<tr>
<td>Punica_granatum</td>
</tr>
<tr>
<td>Quercus_suber</td>
</tr>
<tr>
<td>Rattus_norvegicus</td>
</tr>
<tr>
<td>Rice_gall_dwarf_virus</td>
</tr>
<tr>
<td>Ricinus_communis</td>
</tr>
<tr>
<td>Rosa_chinensis</td>
</tr>
<tr>
<td>Salmo_salar</td>
</tr>
<tr>
<td>Schmallenberg_virus</td>
</tr>
<tr>
<td>Semliki_forest_virus</td>
</tr>
<tr>
<td>Shallot_virus_X</td>
</tr>
<tr>
<td>Sindbis_virus</td>
</tr>
<tr>
<td>Solanum_tuberosum</td>
</tr>
<tr>
<td>Southern_tomato_virus</td>
</tr>
<tr>
<td>Spinacia_oleracea</td>
</tr>
<tr>
<td>Stylonychia_lemnae</td>
</tr>
<tr>
<td>Sulcia_muelleri_strain_CARI</td>
</tr>
<tr>
<td>Sus_scrofa</td>
</tr>
<tr>
<td>Thermincola_potens_strain_JR</td>
</tr>
<tr>
<td>Toscana_virus</td>
</tr>
<tr>
<td>Trichuris_suis</td>
</tr>
<tr>
<td>Triticum_aestivum</td>
</tr>
<tr>
<td>Tupaia_paramyxovirus</td>
</tr>
<tr>
<td>Turnip_crinkle_virus</td>
</tr>
<tr>
<td>Tyto_alba</td>
</tr>
<tr>
<td>Vitis_vinifera</td>
</tr>
<tr>
<td>WU_polyomavirus</td>
</tr>
<tr>
<td>Zea_mays</td>
</tr>
<tr>
<td>Zika_virus</td>
</tr>
<tr>
<td>Zostera_marina</td>
</tr>
</tbody>
</table>
</div>
</div>
<br>
<br>
<button type="button" id="problH" class="btn btn-large btn-light waves-effect" data-toggle="collapse" data-target="#problB" style="z-index: 0;">Problems/Suggestion about PredHPI<span class="btn-label btn-label-right"> <i class="fa fa-arrow-down"></i></span></button>
<div id="problB" class="collapse" style="font-size: 18px;">
<p>If you can't get something to work or you want to suggest something that makes this application works better, the developer would be happy to address any question at crissloaiza@gmail.com or cdloaiza@aggiemail.usu.edu.</p>
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© 2018  |  <a href="https://www.usu.edu" target="_blank">Utah State University</a>  |  <a href="http://bioinfo.usu.edu" target="_blank">Kaundal Bioinformatics Laboratory</a>  |  <a href="https://www.psc.usu.edu" target="_blank">Department of Plants, Soils and Climate</a>  |  <a href="http://www.biosystems.usu.edu" target="_blank">Center for Integrated BioSystems </a>
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