SPALNGenome mapping and spliced alignment of cDNA or amino acid sequenceshttps://github.com/ogotoh/spalnspalnbiotools:spalnver.3.0.8bCommand-line toolhttp://edamontology.org/topic_0102MappingCPerlC++GPL-2.0Maturehttp://edamontology.org/operation_2429Mappinghttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_1234Sequence set (nucleic acid)https://github.com/ogotoh/spalnRepositoryhttps://github.com/ogotoh/spalnGeneral10.1093/nar/gkag35742134803PMC1317563310.1093/bioinformatics/btn4601872804310.1093/nar/gks70822848105PMC348821110.1093/bioinformatics/16.3.1901086901210.1093/bioinformatics/btae51739152995PMC1136180910.1007/978-1-0716-1036-7_53328988710.1093/bioinformatics/btl06716500940Osamu Gotohgotoh.osamu.67a@st.kyoto-u.ac.jphttps://orcid.org/0009-0002-6750-1945Personshicshic is a collection of shims for use in automated workflow compositionhttps://github.com/magnuspalmblad/shicshicbiotools:shicScriptMITFree of chargeOpen accessProteomicsGalaxyMetabolomicshttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3747protXMLhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGFhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0870Sequence distance matrixhttp://edamontology.org/format_1912Nexus formathttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0972Text mining reporthttp://edamontology.org/format_2332XMLhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3475TSVhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0896Protein reporthttp://edamontology.org/format_3475TSVhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttp://edamontology.org/operation_3434Conversionhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3655pepXMLhttps://github.com/magnuspalmblad/shicRepositoryhttps://github.com/magnuspalmblad/shic/blob/main/README.mdGeneralMagnus Palmbladmagnus.palmblad@gmail.comhttps://orcid.org/0000-0002-5865-8994Primary contactVeit Schwämmlehttps://orcid.org/0000-0002-9708-6722Dirk Winkelhardthttps://orcid.org/0000-0001-8770-2221Vedran Kasalicahttps://orcid.org/0000-0002-0097-1056Anna-Lena Lamprechthttps://orcid.org/0000-0003-1953-5606GPCRchimeraDBGPCRchimeraDB: A database to support the design of novel chimeric G-Protein Coupled Receptors (GPCRs) to unravel signaling pathways, characterize key regions and facilitate the design of new receptors for drug discovery. It is the first database to centralize chimeric GPCRs into one central repository, offering extensive descriptions at the sequence, structural, and biophysical levels through user-friendly visualization tools, while linking them to their parent GPCRs. Furthermore, GPCRchimeraDB expands the description of natural GPCRs compared to existing databases like GPCRdb and IUPHAR by including their biophysical profiles and integrating an interactive sequence-structure (1D-3D) visualization tool which helps to keep an overview of the large amount of data. Finally, GPCRchimeraDB incorporates a sequence alignment tool that has been demonstrated to outperform the current state-of-the-art tool for non-conventional GPCRs, which are critical targets in drug discovery.https://bio2byte.be/gpcrchimeradbgpcrchimeradbbiotools:gpcrchimeradb2025-12.v1Database portalhttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_1317Structural biologyhttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_3398BioengineeringCC-BY-4.03D-BioInfo-Protein-Ligand-InteractionsgpcrOpen access3D-BioInfoBelgiumhttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/data_1017Sequence rangehttp://edamontology.org/data_2872ID listhttp://edamontology.org/data_0897Protein propertyhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/data_0970Citation10.1016/j.jmb.2025.16916440268234PrimaryPathoFact2An Integrative Pipeline for Antimicrobial Resistance Genes, Virulence Factors, Toxin-associated proteins, and Biosynthetic Gene Clusters Prediction in Metagenomeshttps://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2pathofact2biotools:pathofact22.0Command-line toolhttp://edamontology.org/topic_4013Antimicrobial resistanceLinuxPythonRBashGPL-3.0Free of chargeOpen accesshttp://edamontology.org/operation_3482Antimicrobial resistance predictionhttp://edamontology.org/operation_3461Virulence predictionhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/data_2976Protein sequencehttps://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2Repositoryhttps://zenodo.org/records/14192463Repositoryhttps://zenodo.org/records/17647372RepositoryLuis F. Delgadoluis.delgado@uni.luhttps://orcid.org/0000-0001-7850-5285Júlia Ortís Sunyerjulia.ortissunyer@uni.luhttps://orcid.org/0000-0002-2714-7067Paul Wilmespaul.wilmes@uni.luhttps://orcid.org/0000-0002-6478-2924BaktaRapid & standardized annotation of bacterial genomes, MAGs & plasmidshttps://github.com/oschwengers/baktabaktabiotools:baktav1.12.0Web applicationCommand-line toolhttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0091BioinformaticsLinuxMacPythonGPL-3.0MatureFree of chargeOpen accessToolsGermanyhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/data_0925Sequence assemblyhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2914Sequence features metadatahttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2012Sequence coordinateshttp://edamontology.org/format_1975GFF3http://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1364Hidden Markov modelhttp://edamontology.org/format_3329HMMER3bakta --db <db-path> --prefix <prefix> --output <output-path> genome.fastahttps://github.com/oschwengers/baktaRepositoryhttps://github.com/oschwengers/bakta/issuesIssue trackerhttps://bioconda.github.io/recipes/bakta/README.htmlOtherhttps://bakta.computational.bioServicehttps://zenodo.org/records/14916843OtherMandatory annotation databasev6.0https://github.com/oschwengers/bakta/blob/main/README.mdGeneralhttps://github.com/oschwengers/bakta/blob/main/CONTRIBUTION.mdContributions policyhttps://github.com/oschwengers/bakta/blob/main/CODE_OF_CONDUCT.mdCode of conducthttps://bakta.readthedocs.io/User manualdiamonduseshmmer3usesinfernalusestrnascan-seusesblastusesaragornusespilercrusesdeepsiguses10.1099/mgen.0.00068534739369PMC8743544Primary1.110.1093/nar/gkaf33540271661PMC12230652PrimaryOliver Schwengersoliver.schwengers@cb.jlug.dehttps://github.com/oschwengershttps://orcid.org/0000-0003-4216-2721PersonPrimary contactDeveloperMaintainerJustus Liebig University Giessenhttps://www.uni-giessen.deInstituteProviderOMAProject that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, it is one of the largest projects of its kind.http://omabrowser.org/oma/home/omabiotools:omaDesktop applicationWeb applicationDatabase portalhttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_0797Comparative genomicsMacLinuxWindowsDataSwitzerlandhttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_3021UniProt accessionhttp://edamontology.org/data_3671Texthttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/data_0842Identifierorthology prediction and paralogy OMA grouphttps://omabrowser.org/oma/about/General10.1093/nar/gku115825399418PMC4383958Primary10.1093/nar/gkad102037962356PMC10767875Primary10.1093/nar/gkaa100733174605PMC7779010Primary10.1093/nar/gkx101929106550PMC5753216PrimarySIBInstituteProvidercontact@omabrowser.orgPersonPrimary contactChristophe DessimozChristophe.Dessimoz@unil.chPersonPrimary contactFastOMAFastOMA is a scalable software package to infer orthology relationship.https://github.com/dessimozlab/FastOMAfastomabiotools:fastoma0.5.1Command-line toolhttp://edamontology.org/topic_0797Comparative genomicsMacLinuxPythonMPL-2.0MatureFree of chargeOpen accessSwitzerlandhttp://edamontology.org/operation_3947Phylogenetic tree reconciliationhttp://edamontology.org/operation_2479Protein sequence analysishttp://edamontology.org/operation_3209Genome comparisonhttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_0540Phylogenetic inference (from molecular sequences)http://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_2200FASTA-like (text)http://edamontology.org/data_3028Taxonomyhttp://edamontology.org/format_1910newickhttps://github.com/dessimozlab/FastOMARepositoryhttps://omabrowser.orgServicehttps://github.com/DessimozLab/FastOMA/blob/main/README.mdQuick start guideomameruses10.1038/s41592-024-02552-839753922PMC11810774ASAFindASAFind is a software that predicts the intracellular location of proteins in cells with four membrane-bound complex plastids of red algal origin.
These plastids evolved via eukaryote-eukaryote endosymbiosis and for example can be found in diatoms and cryptophytes. ASAFind uses protein sequence data and external predictions of signal peptides (by the tools SignalP and TargetP), and predicts plastid proteins, and proteins that are targeted to the periplastidic compartment from these data; optionally, a graphical output can generated.https://asafind.jcu.cz/asafindbiotools:asafind2.0ScriptCommand-line toolWeb servicehttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_0622GenomicsMacLinuxPythonCC-BY-SA-4.0ELIXIR-CZCzech RepublicMatureFree of chargeOpen accessToolsPlant SciencesMarine MetagenomicsMicrobial BiotechnologyCzech Republichttp://edamontology.org/operation_2489Subcellular localisation predictionhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1270Feature tablehttps://asafind.jcu.czServiceWeb Servicehttps://github.com/ASAFind/ASAFind-2RepositoryInformation and source code, for local installation or developmenthttps://asafind.jcu.cz/download-page/Downloads pageDownload page on web-service, links to repository2.0https://asafind.jcu.cz/download-page/Installation instructionssignalpusestargetpuses10.1111/tpj.7013840464854PMC12136025Primary2.0Publication of the current version of ASAFind (2.0)10.1111/tpj.1273425438865PMC4329603Other1.0Publication of the first version of ASAFind10.48550/arXiv.2303.02509Benchmarking study1.0Benchmarking of the performance of the first version of ASAFindMarta Vohnoutovámvohnoutova@jcu.czhttps://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699https://orcid.org/0000-0002-8915-8626PersonContributorDeveloperMaintainerAnsgar Gruberagruber@prf.jcu.czhttps://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401https://orcid.org/0000-0002-5876-4391PersonPrimary contactDeveloperDocumentorprolfquappA command-line tool for differential expression analysis in quantitative proteomicshttps://github.com/prolfqua/prolfquappprolfquappbiotools:prolfquapp0.1.6Command-line toolhttp://edamontology.org/topic_0121ProteomicsMacLinuxRMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_3741Differential protein expression profilinghttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA./prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANN
# and again you run the version within the docker container with
# ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y config.yaml -w NameOfAnalysis -s DIANNhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3620xlsxhttp://edamontology.org/operation_0571Expression data visualisationhttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/format_3475TSVhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/prolfqua/prolfquappRepositoryhttps://github.com/prolfqua/prolfquapp/issuesIssue trackerhttps://github.com/prolfqua/prolfquapp/releases/tag/0.1.6Downloads page0.1.6https://github.com/prolfqua/prolfquapp/blob/master/README.mdGeneral10.1021/acs.jproteome.4c00911Primary0.0.6PeptideShakerPeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics datahttp://compomics.github.io/projects/peptide-shaker.htmlpeptideshakerbiotools:peptideshaker3.0.11Desktop applicationCommand-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0644ProteomeMacLinuxJavaApache-2.0de.NBIProteomicsBioInfra.ProtOpen accesshttp://edamontology.org/operation_3694Mass spectrum visualisationhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_2428Validationhttp://edamontology.org/operation_3755PTM localisationhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_0570Structure visualisationhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0945Peptide identificationhttp://edamontology.org/format_3247mzIdentMLhttp://edamontology.org/data_2536Mass spectrometry datahttp://edamontology.org/format_3651MGFhttps://github.com/compomics/peptide-shakerSource codehttp://compomics.github.io/projects/peptide-shaker.html#read-meGeneral10.1038/nbt.310925574629PrimaryBioInfra.ProtInstituteProviderDominik Kopczynskdominik.kopczynski@isas.dehttp://compomics.github.io/projects/peptide-shaker.htmlPersonPrimary contactNGPSimulation of next-generation proteomics (NGP) based on single-molecule sequencing.https://github.com/magnuspalmblad/NGPngpbiotools:ngphttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA10.1021/acs.jproteome.1c0013633904308PMC8185883PrimaryMS AnnikaMS Annika is a crosslink search engine based on MS Amanda, aimed at identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and MS3 spectra. It can deal with a wide variety of cross-linkers and provides robust and transparent FDR control based on a target-decoy approach. MS Annika is available free of charge as a plug-in for Proteome Discoverer.https://github.com/hgb-bin-proteomics/MSAnnikams_annikabiotools:ms_annikaProteome Discoverer 3.2: MS Annika 3.0 v3.0.7Proteome Discoverer 3.1: MS Annika 3.0 v3.0.7Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4fixProteome Discoverer 2.5: MS Annika 2.0 v1.1.3Proteome Discoverer 2.4: MS Annika v1.0.0Proteome Discoverer 2.3: MS Annika v1.0.0Plug-inhttp://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0736Protein folds and structural domainshttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0091BioinformaticsWindowsC#FreewareMatureFree of chargeOpen accesshttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3646Peptide database searchhttp://edamontology.org/operation_3755PTM localisationhttp://edamontology.org/operation_3645PTM identificationhttp://edamontology.org/operation_3649Target-Decoyhttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_3651MGFhttp://edamontology.org/format_3712Thermo RAWhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttps://github.com/hgb-bin-proteomics/MSAnnikaRepositoryMS Annika version archivehttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.2/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 3.2PD3.2:latesthttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 3.1PD3.1:latesthttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.0/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 3.0PD3.0:latesthttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.5/latest.zipSoftware packageLatest MS Annika version for Proteome Disoverer 2.5PD2.5:latesthttps://hgb-bin-proteomics.github.io/MSAnnika/Generalhttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/MS_Annika_3.0_UserManual.pdfUser manualhttps://github.com/hgb-bin-proteomics/MSAnnika/raw/master/tutorial/MS_Annika_3.0_Tutorial.pdfTraining materialDetailed tutorial how to use MS Annikahttps://www.youtube.com/watch?v=L1lVt35PYv4Training materialDetailed tutorial how to use MS Annikams_amandauses10.1021/acs.jproteome.0c0100033852321PMC8155564Primary1.0MS Annika for cleavable crosslink identification from MS2 spectra10.1021/acs.jproteome.3c0032537566781PMC10476269Primary2.0MS Annika 2.0 for cleavable crosslink identification from MS3 spectra10.1038/s42004-024-01386-x39702463PMC11659399Primary3.0MS Annika 3.0 for non-cleavable crosslink identificationViktoria Dorferviktoria.dorfer@fh-hagenberg.athttp://bioinformatics.fh-hagenberg.at/https://orcid.org/0000-0002-5332-5701PersonPrimary contactMicha Birklbauermicha.birklbauer@fh-hagenberg.athttp://bioinformatics.fh-hagenberg.at/https://orcid.org/0009-0005-1051-179XPersonDeveloperEPIKPrecise and scalable evolutionary placement with informative k-mers.https://github.com/phylo42/EPIKepikbiotools:epik0.2.0Command-line toolhttp://edamontology.org/topic_0084PhylogenyLinuxMacC++PythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_0323Phylogenetic inferencehttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0955Data indexhttp://edamontology.org/format_2333Binary format10.1093/BIOINFORMATICS/BTAD69237975872PMC107010970.2.0Nikolai Romashchenkonromashchenko@lirmm.frhttps://orcid.org/0000-0002-2264-5219PersonEric Rivalsrivals@lirmm.frhttps://orcid.org/0000-0003-3791-3973PersonINPSPredicting the impact of mutations on protein stability from sequencehttps://inpsmd.biocomp.unibo.itinpsbiotools:inps1.0http://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0199Genetic variationMatureFree of chargeOpen accessItalyhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/data_2974Protein sequence (raw)Prediction of the impact of non-synonymous polymorphisms on protein stabilityhttps://inpsmd.biocomp.unibo.it/helpGeneral10.1093/bioinformatics/btv29125957347Primary10.1093/bioinformatics/btw19227153629PrimaryELIXIR-ITA-BOLOGNAhttp://www.biocomp.unibo.itDivisionProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperPrimary contactPiero Farisellipiero.fariselli@unito.itPersonPrimary contactDDGembPredicting the impact of mutations on protein stability from sequence using protein language modelshttps://ddgemb.biocomp.unibo.itddgembbiotools:ddgemb1http://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3325Rare diseasesMatureFree of chargeOpen accessToolsRare Diseases3D-BioInfoItalyhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_3498Sequence variationshttps://ddgemb.biocomp.unibo.it/help/General10.1093/bioinformatics/btaf01939799516PMC11783275PrimaryELIXIR-ITA-BOLOGNAhttps://www.biocomp.unibo.itInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonMaintainerDeveloperPrimary contactINPS-MDPredicting the impact of mutations on protein stability from sequence and structure.http://inpsmd.biocomp.unibo.itinps-mdbiotools:inps-md2.0http://edamontology.org/topic_0130Protein folding, stability and designhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_3325Rare diseasesMatureFree of chargeOpen accessTools3D-BioInfoItalyhttp://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/data_3498Sequence variationsPrediction of the impact of non-synonymous polymorphisms on protein stability from sequence.http://edamontology.org/operation_0250Protein property calculationhttp://edamontology.org/data_1460Protein structurehttp://edamontology.org/data_1008Polypeptide chain IDhttp://edamontology.org/data_3498Sequence variationsPrediction of the impact of non-synonymous polymorphisms on protein stability from structure.https://inpsmd.biocomp.unibo.it/helpGeneral10.1093/bioinformatics/btv29125957347Primary10.1093/bioinformatics/btw19227153629PrimaryELIXIR-ITA-BOLOGNAhttps://www.biocomp.unibo.itInstituteProviderCastrense Savojardocastrense.savojardo2@unibo.ithttps://orcid.org/0000-0002-7359-0633PersonDeveloperPiero Farisellipiero.fariselli@unito.itPersonPrimary contactCastrense Savojardosavojard@biocomp.unibo.ithttp://biocomp.unibo.it/savojard/https://orcid.org/0000-0002-7359-0633PersonPrimary contactMacSyLiba Python package library that allow to model and detect macromolecular systems, genetic pathways… by similarity search in prokaryotes datasets.https://github.com/gem-pasteur/macsylibmacsylibbiotools:macsylib1.0.1Libraryhttp://edamontology.org/topic_0085Functional genomicsLinuxMacPythonGPL-3.0GEM PasteurMatureOpen accesshttp://edamontology.org/operation_3672Gene functional annotationhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/data_3949Profile HMMhttps://github.com/gem-pasteur/macsylibRepositoryhttps://pypi.org/project/MacSyLib/Otherhttps://macsylib.readthedocs.io/en/latest/Otherhttps://github.com/gem-pasteur/macsylibSource code1.0.1https://pypi.org/project/MacSyLib/Software package1.0.1https://macsylib.readthedocs.io/en/latest/GeneralmacsyfinderusedBy10.24072/pcjournal.250Institut Pasteur0495fxg12InstituteMicrobial Evolutionary Genomics Unithttps://research.pasteur.fr/en/team/microbial-evolutionary-genomics/DivisionBioinformatics and Biostatistics HUBhttps://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/DivisionEduardo P.C. Rochahttps://orcid.org/0000-0001-7704-822XPersonPrimary contactSophie Abbyhttps://orcid.org/0000-0002-5231-3346PersonPrimary contactBertrand Néronhttps://orcid.org/0000-0002-0220-0482PersonDeveloperEukCCEukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.https://github.com/EBI-Metagenomics/EukCCeukccbiotools:eukccCommand-line toolhttp://edamontology.org/topic_3174MetagenomicsPythonGPL-3.0http://edamontology.org/operation_3180Sequence assembly validationhttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/data_2886Protein sequence record10.1186/s13059-020-02155-4UniversalMerUniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists.https://ugrammer.github.ioUniversalMerbiotools:UniversalMer2.0.0Command-line toolhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3473Data mininghttp://edamontology.org/topic_0080Sequence analysisWindowsMacC++CFreewareEmergingFree of chargeOpen accessToolsUKhttp://edamontology.org/operation_3472k-mer countinghttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/format_2546FASTA-likehttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_2546FASTA-likehttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_2546FASTA-likehttps://sourceforge.net/projects/universal-mer/Mirrorhttps://sourceforge.net/projects/universal-mer/Command-line specification2.0ProteinPromptA webserver for predicting protein-protein interactions.http://proteinformatics.org/ProteinPromptproteinpromptbiotools:proteinpromptWeb applicationhttp://edamontology.org/topic_0128Protein interactionshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3957Protein interaction experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0154Small moleculesMacLinuxWindowsPythonFree of chargeOpen accesshttp://edamontology.org/operation_2492Protein interaction predictionhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2464Protein-protein binding site predictionhttp://edamontology.org/data_2976Protein sequencehttps://gitlab.hzdr.de/proteinprompt/ProteinPromptRepository10.1101/2021.09.03.458859René Staritzbichlerrene.staritzbichler@medizin.uni-leipzig.dehttps://orcid.org/0000-0002-6719-2997Peter W. Hildebrandhttps://orcid.org/0000-0003-0063-1104Sebastian Canzlerhttps://orcid.org/0000-0001-7935-9582Markus FischerDavid UlbrichtNikola RisticDeepSigPrediction of secretory signal peptides in protein sequenceshttps://busca.biocomp.unibo.it/deepsig/deepsigbiotools:deepsig1.2.5Web applicationCommand-line toolhttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacPythonC++GPL-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 formathttps://github.com/BolognaBiocomp/deepsigSource code1.2.5https://hub.docker.com/r/bolognabiocomp/deepsigContainer file1.2.5https://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 contactBioSurfDBBioSurfDB is a online database for biodegradation and biosurfactants.https://www.biosurfdb.orgbiosurfdbbiotools:biosurfdbDatabase portalhttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_0821EnzymesMatureFree of chargeOpen accesshttp://edamontology.org/operation_0495Local alignmenthttp://edamontology.org/data_3494DNA sequencehttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/operation_0349Sequence database search (by property)10.1093/database/bav033PrimaryJorge S. Oliveirajorge.oliveira@tecnico.ulisboa.pthttps://web.tecnico.ulisboa.pt/jorge.oliveira/https://orcid.org/0000-0001-6425-2176PersonPrimary contactAna Teresa Freitasana.freitas@tecnico.ulisboa.pthttp://orcid.org/0000-0003-4638-2879PersonPrimary contactAna Tereza Ribeiro de Vasconcelosatrv@lncc.brhttp://orcid.org/0000-0002-4632-2086PersonPrimary contactLucymara Fassarella Agnez-Limalucymara.agnez@ufrn.brhttp://orcid.org/0000-0003-0642-3162PersonPrimary contactGil Poiares-Oliveiragpo@biodata.pthttps://web.tecnico.ulisboa.pt/gil.oliveirahttps://orcid.org/0000-0003-4638-2879PersonMaintainerPEP-FOLD4PEP-FOLD4 is a fast and accurate structure prediction tool for peptides of up to 40 amino acids in aqueous solutions. Unlike many machine-learning approaches (e.g., AlphaFold2, TrRosetta, RaptorX), it integrates the Debye-Hückel formalism for charged side-chain interactions with a Mie potential for intramolecular forces. Based on a coarse-grained representation, PEP-FOLD4 performs competitively on well-structured peptides and shows significant improvements for poly-charged peptides, making it particularly useful for studying pH- and salt-dependent conformations.https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4pep-fold4biotools:pep-fold4Web applicationhttp://edamontology.org/topic_2275Molecular modellinghttp://edamontology.org/topic_3332Computational chemistryPythonMatureFree of chargeOpen access3D-BioInfoFrancehttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_0476Ab initio structure predictionhttp://edamontology.org/data_2976Protein sequencehttps://mobyle2.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-FOLD4ServiceLink to the PEP-FOLD4 web page servicehttps://owncloud.rpbs.univ-paris-diderot.fr/owncloud/index.php/s/7NHDSJXiQA0V2zySource codeSource code and recipe for docker images allowing to run PEP-FOLD4 locally. All repository content is covered by a non-commercial license agreement and may be used for non-commercial and internal research purposes only.https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4/User manual10.1093/nar/gkad37637166962PMC10320157PrimaryJulien Reyjulien.rey@u-paris.frhttps://orcid.org/0000-0002-3050-511XPersonSupportDeveloperPrimary contactSamuel Murailsamuel.muriail@u-paris.frhttps://orcid.org/0000-0002-3842-5333PersonContributorSjoerd de Vrieshttps://orcid.org/0000-0002-7701-3454PersonContributorPhilippe Derreumauxphilippe.derreumaux@ibpc.frPersonContributorPierre Tufférypierre.tuffery@inserm.frhttps://orcid.org/0000-0003-1033-9895PersonContributorProteoMakerProteoMaker is a platform for the generation of an in-silico bottom-up proteomics data set with a ground truth on the level of proteoforms.https://github.com/computproteomics/ProteoMakerproteomakerbiotools:proteomakerLibraryWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3524Simulation experimentMacLinuxWindowsRMITProteomicsMatureFree of chargeOpen accesshttp://edamontology.org/operation_3566Simulated gene expression data generationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttps://computproteomics.bmb.sdu.dk/app_direct/ProteoMakerServiceWeb applicationhttps://github.com/computproteomics/ProteoMakerSource codePHIEmbedPHIEmbed is a phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. It presents improvements over using handcrafted (manually feature-engineered) sequence properties and eliminates the need to manually extract and select features from phage sequences.https://github.com/bioinfodlsu/phage-host-predictionphiembedbiotools:phiembedCommand-line toolhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3307Computational biologyhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0781VirologyMacLinuxWindowsPythonMITEmergingFree of chargeOpen accesshttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAPredicts the host genus of a phage given its receptor-binding protein sequenceshttps://github.com/bioinfodlsu/phage-host-predictionRepositoryhttp://phiembed.bioinfodlsu.com/Servicehttps://github.com/bioinfodlsu/phage-host-predictionSource codehttps://github.com/bioinfodlsu/phage-host-predictionInstallation instructionsQuick start guideCitation instructionsCommand-line options10.1371/journal.pone.028903037486915PrimaryMark Edward M. Gonzalesgonzales.markedward@gmail.comhttps://github.com/memgonzaleshttps://orcid.org/0000-0001-5050-3157PersonDeveloperResearch Assistant, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, PhilippinesJennifer C. Uretajennifer.ureta@gmail.comhttps://scholar.google.com/citations?user=v0Tf_u4AAAAJ&hl=enhttps://orcid.org/0000-0003-0427-5311PersonContributorFaculty, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, PhilippinesAnish M.S. Shresthaanish.shrestha@dlsu.edu.phhttps://a-transposable-element.com/https://orcid.org/0000-0002-9192-9709PersonPrimary contactHead, Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, PhilippinesDynaMineProtein backbone dynamics prediction from sequence.http://dynamine.ibsquare.be/dynaminebiotools:dynamine1Web APIWeb applicationhttp://edamontology.org/topic_3306Biophysicshttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_3538Protein disordered structureLinuxWindowsMachttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_1929FASTAProtein backbone dynamics prediction from sequence File containing one value per amino acid in each protein sequencehttp://dynamine.ibsquare.be/help/General10.1038/ncomms374124225580Other10.1093/nar/gku27024728994PMC4086073Othervub.ac.beInstituteProviderWim Vrankenwvranken@vub.ac.beSupportWim Vrankenwvranken@vub.ac.bePersonPrimary contactTREND Protein Evolution FunctionTREND is a platform that allows researchers to explore protein function and evolution identifying protein features, gene neighborhoods and operons, clustering neighboring genes, and integrating all these data into phylogenomic context and cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides ample opportunities for adjusting each step of the analysis.http://trend.evobionet.com/trend_protein_evolution_functionbiotools:trend_protein_evolution_functionWeb servicehttp://edamontology.org/topic_3299Evolutionary biologyhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_3301Microbiologyhttp://edamontology.org/topic_3510Protein sites, features and motifshttp://edamontology.org/topic_0085Functional genomicshttp://edamontology.org/topic_0194Phylogenomicshttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_0323Phylogenetic inferencehttp://edamontology.org/operation_0291Sequence clusteringhttp://edamontology.org/operation_2995Sequence classificationhttp://edamontology.org/operation_0246Protein domain recognitionhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_1384Protein sequence alignmenthttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1929FASTAhttp://edamontology.org/data_0872Phylogenetic treehttp://edamontology.org/format_1910newickhttp://edamontology.org/data_1900NCBI locus taghttp://edamontology.org/format_2330Textual formathttp://edamontology.org/data_2385RefSeq accession (protein)http://trend.evobionet.com/helpUser manual10.1093/nar/gkaa24332282909PMC7319448Primary10.1093/nar/gkac03435100406PMC8860576OtherCan be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937Vadim Gumerovgumerov.1@osu.eduhttps://orcid.org/0000-0003-1670-7679SVMHCPrediction of MHC class I binding peptides.http://www.sbc.su.se/%7Epierre/svmhc/svmhcbiotools:svmhc1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence10.1186/1471-2105-3-2512225620PMC129981Primarybils.seInstituteProviderarne@bioinfo.sePersonPrimary contactMDR databaseMedium-chain dehydrogenases/reductases database.http://www.bioinfo.ifm.liu.se/services/mdr/mdrbiotools:mdrDatabase portalhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence10.1110/ps.035428.10818614751PMC2548362Primarybils.seInstituteProvideryohell@ifm.liu.sePersonPrimary contactDRIP-PREDDisorder/order prediction for proteins.http://www.sbc.su.se/%7Emaccallr/disorder/cgi-bin/submit.cgidrip-predbiotools:drip-pred1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequence10.1007/s10858-009-9386-z19915800PMC2797623Otherbils.seInstituteProvidermaccallr@sbc.su.sePersonPrimary contactmsaDisplay multiple-sequence alignment. The tool is also available as R/BioConductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms.http://msa.biojs.netmsabiotools:msa1.0.0Command-line toolLibraryhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_3168SequencingLinuxWindowsMacJavaScriptApache-2.0Rostlab toolsBioconductorBioJSMatureFree of chargehttp://edamontology.org/operation_0564Sequence visualisationhttp://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_1982ClustalW formathttp://edamontology.org/format_1984FASTA-alnVisualizes multiple sequence alignment, calculates conservation, shows sequence logo, applies multiple color schemes A multiple sequence alignment (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment Images are exported in PNG Export sequences in FASTA format Export features in GFF
NOTE: Actually, all these output types of data should instead be under separate "constant" operations, while the visualisation should be an unary operation, perhaps without an output.http://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1948nbrf/pirhttp://edamontology.org/format_1929FASTAhttp://edamontology.org/format_1935GCGhttp://edamontology.org/format_1997PHYLIP formathttp://edamontology.org/format_1927EMBL formathttp://edamontology.org/format_1936GenBank formathttps://github.com/wilzbach/msaRepositoryhttp://biojs.io/Software cataloguehttp://github.com/wilzbach/msaHelpdeskhttp://www.bioinf.jku.at/software/msa/Mirrorhttps://github.com/wilzbach/msaSource codehttps://cdn.bio.sh/Binarieshttps://github.com/wilzbach/msa/blob/master/LICENSETerms of usehttp://msa.biojs.netGeneral10.1093/bioinformatics/btw47427412096PMC5181560Primary10.1093/bioinformatics/btv49426315911OtherSebastian WilzbachPersonDeveloperIan SillitoeContributorGuy YachdavContributorBenedikt RauscherContributorTatyana GoldbergContributorTechnische Universität MünchenInstituteProviderGoogle Summer of Code (GSoC) 2014Funding agencyContributorBioJSInstituteProviderhttp://github.com/wilzbach/msaPersonPrimary contactUlrich Bodenhoferbodenhofer@bioinf.jku.atPersonPrimary contactTreeFamSearch of TreeFam's HMM collection, allows query sequence to be aligned (MAFFT) and inserted into tree (RAxML) to significantly matching models.http://www.treefam.org/searchtreefambiotools:treefam1Web applicationhttp://edamontology.org/topic_0084Phylogenyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0623Gene and protein familiesLinuxWindowsMacEBI Toolshttp://edamontology.org/operation_0323Phylogenetic tree generationhttp://edamontology.org/operation_0239Sequence motif recognitionhttp://edamontology.org/data_2976Protein sequencehttps://treefam.tenderapp.com/Helpdeskhttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.treefam.org/helpGeneral10.1093/nar/gkj11816381935PMC1347480OtherFabian SchreiberPersonDeveloperMateus PatricioPersonDeveloperEMBL-EBIInstituteProviderhttps://treefam.tenderapp.com/PersonPrimary contactFabian Schreiberfs@ebi.ac.ukPersonPrimary contactLigSearchIdentifies small molecules likely to bind to given protein.http://www.ebi.ac.uk/thornton-srv/databases/LigSearchligsearchbiotools:ligsearch1Web applicationhttp://edamontology.org/topic_2814Protein structure analysishttp://edamontology.org/topic_0128Protein interactionsLinuxWindowsMacThornton ToolsEBI Toolshttp://edamontology.org/operation_2575Protein binding site predictionhttp://edamontology.org/data_2976Protein sequencehttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/thornton-srv/databases/LigSearchGeneral10.1107/s090744491302229424311580PMC3852652Roman LaskowskiPersonDeveloperTjaart de BeerPersonDeveloperThornton GroupPersonDeveloperEMBL-EBIInstituteProvidertjaart@ebi.ac.ukPersonPrimary contactRoman Laskowskiroman@ebi.ac.ukPersonPrimary contactSASAnnotation of protein sequence with structural info from similar proteins in the PDB.http://www.ebi.ac.uk/thornton-srv/databases/sassasbiotools:sas1Web applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxWindowsMacThornton ToolsEBI Toolshttp://edamontology.org/operation_0346Sequence similarity searchhttp://edamontology.org/operation_3092Protein feature detectionhttp://edamontology.org/data_2976Protein sequenceThe ouput is an alignment of the query sequence vs a sequence from PDB, annotated by structural datahttp://www.ebi.ac.uk/about/terms-of-useTerms of usehttp://www.ebi.ac.uk/thornton-srv/databases/sasGeneral10.1093/protein/11.10.8559862203PrimaryRoman LaskowskiPersonDeveloperThornton GroupPersonDeveloperDuncan MilburnContributorEMBL-EBIInstituteProviderroman@ebi.ac.ukPersonPrimary contactRoman Laskowskiroman@ebi.ac.ukPersonPrimary contactTabhuWeb server for antibody humanisation specifically designed to help researcher in each step of a humanisation experiment. It provides tools to: Select the suitable humane template; Select the grafting region; Predict the non-human and humanised antibody paratope; Select the minimum set of back-mutations to retain the parental binding affinity; Build the three-dimensional humanised antibody model and check its structure.http://www.biocomputing.it/tabhutabhubiotools:tabhu1.0Web applicationhttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMachttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/data_2976Protein sequenceTool for AntiBody Humanizationhttp://circe.med.uniroma1.it/tabhu/help.phpGeneral10.1093/bioinformatics/btt36923803466PMC3753563PrimaryELIXIR-ITA-SAPIENZAInstituteProviderPier Paolo Olimpieripierpaolo.olimpieri@gmail.comPersonPrimary contactDIGITA database of immunoglobulin variable domain sequences and related search and modelling tools.http://www.biocomputing.it/digit/digitbiotools:digitDatabase portalhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0082Structure predictionLinuxWindowsMachttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/operation_0361Sequence annotationhttp://edamontology.org/data_2976Protein sequenceA database of immunoglobulin variable domain sequences and related search and modelling toolshttp://circe.med.uniroma1.it/digit/about.phpGeneral10.1093/nar/gkr80622080506PMC3245095PrimaryELIXIR-ITA-SAPIENZAInstituteProviderPaolo Marcatilipaolo.marcatili@gmail.comPersonPrimary contactPROFaccSolvent accessibility predictor.http://ppopen.informatik.tu-muenchen.de/profaccbiotools:profacc1.0.42Command-line toolWeb applicationhttp://edamontology.org/topic_2814Protein structure analysisLinuxWindowsMacGPL-2.0Rostlab toolsPredictProteinFree of chargehttp://edamontology.org/operation_0384Accessible surface calculationhttp://edamontology.org/data_2974Protein sequence (raw)http://edamontology.org/format_2200FASTA-like (text)https://predictprotein.orgGeneral10.1093/nar/gku36624799431PMC4086098PrimaryBurkhard RostPersonDeveloperChris SanderContributorEMBL HeidelbergInstituteProviderRostLabInstituteProviderhelp@predictprotein.orgPersonPrimary contactLocTree3Prediction of protein subcellular localization in 18 classes for eukaryota, 6 for bacteria and 3 for archaea.https://rostlab.org/services/loctree3/loctree3biotools:loctree31.0.8Command-line toolWeb applicationhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0123Protein propertieshttp://edamontology.org/topic_2229Cell biologyLinuxPHPJavaPerlJavaScriptGPL-3.0Rostlab toolsPredictProteinMatureFree of chargehttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAPrediction of protein sucellular localization in 18 classes for eukaryota, 6 classes for bacteria and 3 for archaea using homology searches (PSI-BLAST) and machine learning (SVM) User can provide one or more sequences in FASTA format The prediction output contains: prediction score, from 1 (weak prediction) to 100 (strong prediction); one of 18 localization classes for eukaryota, 6 for bacteria and 3 for archaea; GO identifier; GO term; prediction source (PSI-BLAST or SVM)https://rostlab.org/owiki/index.php/PackagesRepositoryhttps://rostlab.org/owiki/index.php/PackagesSource codehttps://rostlab.org/owiki/index.php/PackagesBinarieshttps://rostlab.org/owiki/index.php/Loctree3General10.1093/nar/gku39624848019PMC4086075Primary10.1093/bioinformatics/bts39022962467PMC3436817OtherMaximilian HechtPersonDeveloperGuy YachdavPersonDeveloperTimothy KarlPersonDeveloperTobias HampPersonDeveloperTatyana GoldbergPersonDeveloperBurkhard RostContributorHenrik NielsenContributorTechnische Universität MünchenInstituteProviderAlexander von Humboldt Foundation through German Federal Ministry for Education and ResearchFunding agencyContributorErnst Ludwig Ehrlich StudienwerkFunding agencyContributorRostLabInstituteProviderlocalization@rostlab.orghttps://rostlab.org/services/loctree3/PersonPrimary contactSWIPETool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs.http://dna.uio.no/swipeswipebiotools:swipe2.0.5Command-line toolhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3047Molecular biologyLinuxC++AGPL-3.0MatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/data_2977Nucleic acid sequencehttps://github.com/torognes/swipeRepositoryhttps://github.com/torognes/swipeSource codehttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-221Citation instructionshttp://dna.uio.no/swipe/General10.1186/1471-2105-12-22121631914PMC3120707PrimaryTorbjørn RognesPersonDeveloperUiOInstituteProvidertorognes@ifi.uio.noPersonPrimary contactJAliAlignment method for comparing a protein sequence to a protein family, represented by a multiple alignment. It can also be used for sensitive protein database searches. The algorithm is a generalization of the Smith-Waterman algorithm.http://bibiserv.cebitec.uni-bielefeld.de/jalijalibiotools:jali1.3Web APIWeb applicationCommand-line toolhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacCBiGide.NBIMatureFree of chargehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_3154Protein alignmenthttp://edamontology.org/format_1929FASTAComputes Jumping ALIgnments from a protein sequence and an alignment of a protein family.http://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_downloadRepositoryhttp://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_downloadSource codehttp://bibiserv.cebitec.uni-bielefeld.de/resources/download/jaliBinarieshttp://bibiserv.cebitec.uni-bielefeld.de/jali?id=jali_view_manualGeneral10.1089/10665270276103417212487762PrimaryJens StoyePersonDeveloperCeBiTecInstituteProviderBielefeld UniversityInstituteProviderBiBiServInstituteProviderbibi-help@cebitec.uni-bielefeld.dePersonPrimary contactMetaDisorderPrediction method that molds various sources of information predominantly obtained from orthogonal prediction methods which focus on different types of disordered regions.https://github.com/Rostlab/MetaDisordermetadisorderbiotools:metadisorder1Command-line toolhttp://edamontology.org/topic_0091BioinformaticsLinuxMacPerlhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAhttps://github.com/Rostlab/MetaDisorderGeneral10.1186/1471-2105-13-11122624656PMC3465245Primarymytum.deInstituteProviderhttps://rostlab.orgPersonPrimary contactSNAP2Method that predicts the effects of single amino acid substitutions in a protein on the protein's function using neural networks.https://github.com/Rostlab/SNAP2snap2biotools:snap21Command-line toolWeb applicationhttp://edamontology.org/topic_2885DNA polymorphismLinuxMachttp://edamontology.org/operation_0484SNP detectionhttp://edamontology.org/data_2886Protein sequence recordhttp://edamontology.org/format_1929FASTAPrediction of SNP influence on protein function between neutral and effect. "functional effect"-score between -100 (neutral) and 100 (effect) for every possible SNP at every position of the input sequencehttps://github.com/Rostlab/SNAP2Repositoryhttps://github.com/Rostlab/SNAP2Source codehttps://github.com/Rostlab/SNAP2Binarieshttps://github.com/Rostlab/SNAP2Citation instructionsGeneral10.1186/1471-2164-16-s8-s126110438PMC4480835Maximilian HechtPersonDevelopermytum.deInstituteProviderRostlabassistant@rostlab.orghttps://rostlab.orgPersonPrimary contactTOPCONSConsensus prediction of membrane protein topology.http://topcons.cbr.su.se/topconsbiotools:topcons1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMacJavahttp://edamontology.org/operation_0270Transmembrane protein analysishttp://edamontology.org/data_2976Protein sequencehttp://topcons.cbr.su.se/pred/help/General10.1093/nar/gkv48525969446PMC4489233Primarybils.seInstituteProviderarne@bioinfo.sePersonPrimary contactSCAMPIPrediction of membrane protein topology from first principles.http://scampi.cbr.su.se/scampibiotools:scampi1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_0270Transmembrane protein analysishttp://edamontology.org/data_2976Protein sequencehttp://scampi.cbr.su.se/pred/help/General10.1093/bioinformatics/btv70926644416Primarybils.seInstituteProviderarne@bioinfo.sePersonPrimary contactPON-P2Predicts the pathogenicity of amino acid substitutions.http://structure.bmc.lu.se/PON-P2/pon-p2biotools:pon-p21Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_3461Virulence predictionhttp://edamontology.org/data_2886Protein sequence recordhttp://structure.bmc.lu.se/PON-P2/instructions.html/General10.1186/s12920-015-0125-x26282678PMC4539680Primarybils.seInstituteProviderproteinbioinformatik@med.lu.sePersonPrimary contactPON-DisoA method to predict changes in disorder regions contained in protein caused by amino acid substitutions.http://structure.bmc.lu.se/PON-Diso/pon-disobiotools:pon-diso1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2886Protein sequence recordhttp://structure.bmc.lu.se/PON-Diso/instructions.htmlGeneral10.1002/humu.2260024915749Reviewbils.seInstituteProviderproteinbioinformatik@med.lu.sePersonPrimary contactOnD-CRFPredicting order and disorder in proteins using conditional random fields.http://babel.ucmp.umu.se/ond-crf/ond-crfbiotools:ond-crf1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequencehttp://babel.ucmp.umu.se/ond-crf/about.phpGeneral10.1093/bioinformatics/btn261PMC3139103Primarybils.seInstituteProvideruwe@ucmp.umu.sePersonPrimary contactOCTOPUSPrediction of membrane protein topology and signal peptides.http://octopus.cbr.su.se/octopusbiotools:octopus1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_0270Transmembrane protein analysishttp://edamontology.org/data_2976Protein sequencehttp://octopus.cbr.su.se/index.php?about=helpGeneral10.1093/bioinformatics/btn22118474507Primarybils.seInstituteProviderarne@bioinfo.sePersonPrimary contactFragHMMentResidue-residue contact prediction.http://predictioncenter.org/Services/FragHMMent/descr.htmlfraghmmentbiotools:fraghmment1Web applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacJavahttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequencehttp://predictioncenter.org/Services/FragHMMent/descr.htmlGeneral10.1093/bioinformatics/btp14919289446PMC2677742Primarybils.seInstituteProvidertorgeir.hvidsten@umu.sePersonPrimary contactFISH - sequence searchFamily Identification with Structure Anchored Hidden Markov Models.http://babel.ucmp.umu.se/fish/hmmpfam.htmfish_sequence_searchbiotools:fish_sequence_search1Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxWindowsMachttp://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2976Protein sequencehttp://babel.ucmp.umu.se/fish/about.phpGeneral10.1093/nar/gkl33016844969PMC1538871Primarybils.seInstituteProvideruwe@ucmp.umu.sePersonPrimary contact