NetAllergenNetAllergen-1.0 is a predictive model based on the random forest algorithm. It incorporates novel MHC class II presentation propensity features to improve the allergenicity prediction.https://services.healthtech.dtu.dk/services/NetAllergen-1.0/netallergenbiotools:netallergenWeb applicationhttp://edamontology.org/topic_2830Immunoproteins and antigenshttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_0154Small moleculesMacLinuxWindowsFree of chargeOpen accesshttp://edamontology.org/operation_0252Peptide immunogenicity predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0452Indel detectionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA10.1093/BIOADV/VBAD15137901344PMC10603389Carolina Barracarolet@dtu.dkhttps://orcid.org/0000-0002-6836-4906PersonYuchen LiPersonPredGPIPrediction system for GPI-anchored proteins.https://busca.biocomp.unibo.it/predgpipredgpibiotools:predgpi1.0Web applicationhttp://edamontology.org/topic_3542Protein secondary structurehttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacBologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_3351Molecular surface analysishttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2331HTMLPredictionhttps://busca.biocomp.unibo.it/predgpiGeneral10.1186/1471-2105-9-392PrimaryELIXIR-ITA-BOLOGNAInstituteProviderAndrea Pierleoniandrea@biocomp.unibo.itPersonPrimary contactRita Casadiocasadio@biocomp.unibo.itPersonPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonMaintainerDisLocatePrediction of cysteine connectivity patterns in a protein chain.https://busca.biocomp.unibo.it/dislocatedislocatebiotools:dislocate1.0Web applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_3542Protein secondary structureLinuxWindowsMacBologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_1830Free cysteine detectionhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_1829Cysteine bridge detectionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2331HTMLPredictionhttps://busca.biocomp.unibo.it/dislocate/methodGeneral10.1093/bioinformatics/btr38721715467Primary10.1186/1471-2105-14-S1-S1023368835PMC3548674Other10.1007/978-3-642-21946-7_8OtherELIXIR-ITA-BOLOGNAInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttp://biocomp.unibo.it/savojard/https://orcid.org/0000-0002-7359-0633PersonPrimary contactDeveloperMaintainerSChloroPrediction of protein sub-chloroplastinc localization.https://busca.biocomp.unibo.it/schloroschlorobiotools:schloro1Web applicationCommand-line toolhttp://edamontology.org/topic_0140Protein targeting and localisationhttp://edamontology.org/topic_0780Plant biologyLinuxWindowsMacGPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2955Sequence reporthttp://edamontology.org/format_2331HTMLhttps://github.com/BolognaBiocomp/schloroSource codehttps://hub.docker.com/r/bolognabiocomp/schloroContainer filehttps://schloro.biocomp.unibo.it/sclpred/default/indexGeneralhttps://github.com/BolognaBiocomp/schloroCommand-line options10.1093/bioinformatics/btw65628172591PMC5408801PrimaryELIXIR-ITA-BOLOGNAhttp://www.biocomp.unibo.itInstituteMaintainerCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperPrimary contactMaintainerDeepSigPrediction of secretory signal peptides in protein sequenceshttps://busca.biocomp.unibo.it/deepsig/deepsigbiotools:deepsig1.0Web applicationCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacGPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2331HTMLhttps://github.com/BolognaBiocomp/deepsigSource code1.2.5https://hub.docker.com/r/bolognabiocomp/deepsigContainer filehttps://github.com/BolognaBiocomp/deepsigCommand-line options10.1093/bioinformatics/btx81829280997PMC5946842Primary1.0ELIXIR-ITA-BOLOGNAhttp://biocomp.unibo.itInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttp://biocomp.unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactBetAwareA software package for the analysis of TransMembrane β-barrel proteins.https://busca.biocomp.unibo.it/betawarebetawarebiotools:betaware1.0Command-line toolWeb applicationhttp://edamontology.org/topic_0082Structure predictionhttp://edamontology.org/topic_3542Protein secondary structureLinuxWindowsMacPythonGPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_0269Transmembrane protein predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0889Structural profilehttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2330Textual formatPredictionhttps://github.com/BolognaBiocomp/betawareSource codehttps://busca.biocomp.unibo.it/betaware/method/Citation instructionshttps://github.com/BolognaBiocomp/betawareCommand-line optionsbetaware-deephasNewVersion10.1093/bioinformatics/bts72823297037Primary10.1093/bioinformatics/btr549Other10.1186/1748-7188-4-13OtherELIXIR-ITA-BOLOGNAInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttp://biocomp.unibo.it/savojard/https://orcid.org/0000-0002-7359-0633PersonPrimary contactDeveloperMaintainerProteinorthoProteinortho is a tool to detect orthologous genes within different specieshttps://gitlab.com/paulklemm_PHD/proteinorthoproteinorthobiotools:proteinortho6.3.1Command-line toolWorkflowhttp://edamontology.org/topic_0797Comparative genomicsLinuxMacWindowsPerlC++PythonGPL-2.0MatureFree of chargeOpen accesshttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_2403Sequence analysishttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2048Reporthttp://edamontology.org/format_3475TSVhttp://edamontology.org/format_2331HTMLhttp://edamontology.org/format_2332XMLproteinortho input/*.faahttps://gitlab.com/paulklemm_PHD/proteinorthoRepositoryhttps://gitlab.com/paulklemm_PHD/proteinortho/-/issues?sort=created_date&state=openedIssue trackerhttps://toolshed.g2.bx.psu.edu/repository?repository_id=584d8accff31aefeGalaxy servicehttps://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zipSource codeDownload and unpack, compile with `make all`latesthttps://packages.debian.org/unstable/proteinorthoDownloads pageInstallation with dpkg (root privileges are required)https://anaconda.org/bioconda/proteinorthoDownloads pageconda install proteinorthohttps://formulae.brew.sh/formula/proteinorthoDownloads pagebrew install proteinorthohttps://gitlab.com/paulklemm_PHD/proteinortho/-/releasesRelease noteshttps://gitlab.com/paulklemm_PHD/proteinortho/-/wikis/homeFAQhttps://gitlab.com/paulklemm_PHD/proteinorthoGeneralDiamondusesBLASTuses10.3389/fbinf.2023.1322477Primaryversion 6For the version 6 of proteinortho10.1186/1471-2105-12-12421526987PMC3114741version 4 to 5For version 4 to 5 of proteinortho10.1371/journal.pone.0105015OtherThe synteny extension PoFF (-syteny option)Marcus LechnerPersonPrimary contactMaintainerPaul Klemmhttps://gitlab.com/paulklemmhttps://orcid.org/0000-0002-3609-5713PersonMaintainerTPpred 2.0Mitochondrial targeting peptide prediction.https://tppred2.biocomp.unibo.ittppred_2.0biotools:tppred_2.02.0Command-line toolWeb applicationhttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0140Protein targeting and localisationLinuxWindowsMacPythonGPL-3.0Bologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/operation_0253Sequence feature detectionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2331HTMLPredictionhttp://biocomp.unibo.it/savojard/tppred2.tar.gzSource codehttps://tppred3.biocomp.unibo.it/tppred3/default/helpGeneralhttps://tppred2.biocomp.unibo.it/tppred2/default/softwareCommand-line optionsInstallation instructionstppred_1.0isNewVersionOftppred_3.0hasNewVersion10.1093/bioinformatics/btu41124974200Primary10.1093/bioinformatics/btt08923428638PrimaryELIXIR-ITA-BOLOGNAInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperRita Casadiorita.casadio@unibo.itPersonPrimary contactPiero Farisellipiero.fariselli@unito.itPersonPrimary contactCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonPrimary contactMemLociPredictor for the subcellular localization of proteins associated or inserted in eukaryotes membranes.https://mu2py.biocomp.unibo.it/memlocimemlocibiotools:memloci1.0Web applicationhttp://edamontology.org/topic_0140Protein targeting and localisationhttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/topic_0621Model organismsLinuxWindowsMacBologna Biocomputing GroupMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1277Protein featureshttp://edamontology.org/format_2330Textual formatPredictionhttps://mu2py.biocomp.unibo.it/memloci/default/infoGeneral10.1093/bioinformatics/btr108PrimaryELIXIR-ITA-BOLOGNAInstituteProviderAndrea Pierleoniandrea@biocomp.unibo.itPersonPrimary contactPier Luigi Martellipierluigi.martelli@unibo.ithttps://orcid.org/0000-0002-0274-5669PersonPrimary contactCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonMaintainerMemPypePrediction of topology and subcellular localization of Eukaryotic membrane proteins.https://mu2py.biocomp.unibo.it/mempypemempypebiotools:mempype1.0Web applicationhttp://edamontology.org/topic_0140Protein targeting and localisationhttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/topic_0621Model organismsLinuxWindowsMacBologna Biocomputing GroupMatureFree of chargeItalyhttp://edamontology.org/operation_0468Protein secondary structure prediction (helices)http://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_2331HTMLPredictionhttps://mu2py.biocomp.unibo.it/mempype/default/helpGeneral10.1093/nar/gkr282PrimaryELIXIR-ITA-BOLOGNAInstituteProviderAndrea Pierleoniandrea@biocomp.unibo.itPersonPrimary contactPier Luigi Martellipierluigi.martelli@unibo.itPersonPrimary contactCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonMaintainer