NetStartPrediction of eukaryotic translation initiation sites using a protein language model.
NetStart 2.0 is a deep learning-based model that predicts canonical translation initiation sites in mRNA transcripts in species across the eukaryotic domain, including vertebrates, invertebrates, plants, fungi, and protists.
The model integrates the ESM-2 protein language model for assessing transitions from non-coding to coding regions with local start codon sequence context and taxonomical information. It has been trained on sequences from 60 phylogenetically diverse eukaryotic species.
If you need help with the bioinformatics programs, see the "Getting Help" section at the server site at the link.https://services.healthtech.dtu.dk/services/NetStart-2.0/netstart_2.0biotools:netstart_2.02.0http://edamontology.org/topic_3512Gene transcriptshttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0621Model organismsMacLinuxPythonhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_0362Genome annotationhttp://edamontology.org/operation_0477Protein modellinghttp://edamontology.org/operation_0439Translation initiation site predictionhttp://edamontology.org/data_3495RNA sequencehttp://edamontology.org/format_1929FASTAhttps://github.com/lsandvad/netstart2RepositoryGitHub with code and instructions and to download and run the program locallyhttps://services.healthtech.dtu.dk/services/NetStart-2.0/ServiceNetStart 2.0 server where sequences can be uploaded directly without having to download the program (hosted by DTU Health Tech).10.1186/S12859-025-06220-240830753PMC12366053Method2.0Line Sandvad Nielsenline.s.nielsen@bio.ku.dkPersonHenrik Nielsenhenni@dtu.dkPersonFeaturePComparative analysis of protein sequences derived from the same transcript by alternative splicing, genome variation data (SNPs) or protein families from one or more organisms.http://cbs.dtu.dk/services/EPipe/featurepbiotools:featurep0.983Web applicationWeb servicehttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_2451Sequence comparisonhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/EPipe/instructions.phpGeneral10.1016/j.sbi.2010.03.00820403684PrimaryCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkPersonPrimary 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 contactSecretomePPredictions of non-classical (i.e. not signal peptide triggered) protein secretion.http://cbs.dtu.dk/services/SecretomeP/secretomepbiotools:secretomep2.0Command-line toolWeb applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTApredicts of non-classical protein secretionhttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/SecretomeP/instructions.phpGeneral10.1093/protein/gzh03715115854Other10.1186/1471-2180-5-5816212653PMC1266369OtherCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkPersonPrimary contactNikolaj Sorgenfrei Blomnblom@kt.dtu.dkhttp://orcid.org/0000-0001-7787-7853PersonNetSolPPrediction of solubility and usability of proteins expressed in E. colihttps://services.healthtech.dtu.dk/service.php?NetSolPnetsolpbiotools:netsolpWeb applicationhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_3068Literature and languageMacLinuxWindowsFree of chargeOpen accesshttp://edamontology.org/operation_0409Protein solubility predictionhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTA10.1093/bioinformatics/btab80135088833Alexander Rosenberg Johansenhttps://orcid.org/0000-0002-4993-7916Henrik Nielsenhttps://orcid.org/0000-0002-9412-9643Jose J Almagro Armenteroshttps://orcid.org/0000-0003-0111-1362NetSurfP-3.0Accurate and fast prediction of protein structural features by protein language models and deep learning.https://services.healthtech.dtu.dk/service.php?NetSurfP-3.0netsurfp-3.0biotools:netsurfp-3.0Web applicationhttp://edamontology.org/topic_3542Protein secondary structurehttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3297Biotechnologyhttp://edamontology.org/topic_0166Protein structural motifs and surfaceshttp://edamontology.org/topic_0082Structure predictionMacLinuxWindowsFree of chargeOpen accesshttp://edamontology.org/operation_2488Protein secondary structure comparisonhttp://edamontology.org/operation_0267Protein secondary structure predictionhttp://edamontology.org/operation_0249Protein geometry calculationhttp://edamontology.org/data_2976Protein sequencehttp://edamontology.org/format_1929FASTAhttps://dtu.biolib.com/nsp3Other10.1093/nar/gkac43935648435PMC9252760Paolo Marcatilipaolo.marcatili@gmail.comhttps://orcid.org/0000-0003-2615-5695PersonJeppe Hallgrenhttps://orcid.org/0000-0001-5377-2643Henrik Nielsenhttps://orcid.org/0000-0002-9412-9643Ole Wintherhttps://orcid.org/0000-0002-1966-3205Morten Nielsenhttps://orcid.org/0000-0001-7885-4311Bent Petersenhttps://orcid.org/0000-0002-2472-8317Magnus Haraldson Høiehttps://orcid.org/0000-0003-2567-758XErik Nicolas KiehlDeepLocPrediction of eukaryotic protein subcellular localization using deep learning.http://www.cbs.dtu.dk/services/DeepLoc/deeplocbiotools:deeploc1.0Web servicehttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0123Protein propertiesLinuxWindowsMacOtherMaturehttp://edamontology.org/operation_2489Protein subcellular localisation predictionhttp://edamontology.org/data_1233Sequence set (protein)http://edamontology.org/format_1929FASTAhttp://www.cbs.dtu.dk/services/DeepLoc/instructions.phpUser manual10.1093/bioinformatics/btx43129036616Henrik Nielsenhnielsen@cbs.dtu.dkPersonPrimary contactSignalPPrediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms.http://cbs.dtu.dk/services/SignalP/signalpbiotools:signalp4.1rrid:SCR_015644rridCommand-line toolWeb applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxMacOtherCBSMatureFree of charge (with restrictions)http://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTApredicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organismshttp://www.cbs.dtu.dk/cgi-bin/sw_request?signalpRepositoryhttp://www.cbs.dtu.dk/cgi-bin/sw_request?signalpSource codehttp://www.cbs.dtu.dk/cgi-bin/sw_request?signalpBinarieshttp://www.cbs.dtu.dk/services/SignalPGeneral10.1038/nmeth.170121959131PrimaryTN PetersenPersonDeveloperCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643DeveloperHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643PersonPrimary contactTatPPrediction of the presence and location of Twin-arginine signal peptide cleavage sites in bacteria.http://cbs.dtu.dk/services/TatP/tatpbiotools:tatp1.0Web applicationWeb servicehttp://edamontology.org/topic_0160Sequence sites, features and motifsLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_0418Protein signal peptide detectionhttp://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTApredicts the presence and location of Twin-arginine signal peptide cleavage sites in bacteria. Signal peptide/non-signal peptide prediction based on a combination of two artificial neural networkshttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/TatP/instructions.phpGeneral10.1186/1471-2105-6-16715992409PMC1182353PrimaryCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643PersonPrimary contactNetAcetPrediction of substrates of N-acetyltransferase A (NatA).http://cbs.dtu.dk/services/NetAcet/netacetbiotools:netacet1.0Web applicationhttp://edamontology.org/topic_0080Sequence analysisLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_2423Prediction and recognitionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTApredicts substrates of N-acetyltransferase A (NatA)http://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/NetAcet/General10.1093/bioinformatics/bti13015539450PrimaryCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkPersonPrimary contactNicolaj Sorgenfrei Blomnblom@kt.dtu.dkhttp://orcid.org/0000-0001-7787-7853PersonTargetPPrediction of the subcellular location of eukaryotic proteins.http://cbs.dtu.dk/services/TargetP/targetpbiotools:targetp1.1Command-line toolWeb applicationWeb servicehttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxOtherEmergingFree of charge (with restrictions)http://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAPredicts the subcellular location of eukaryotic proteinshttp://cbs.dtu.dk/servicesSoftware cataloguehttp://www.cbs.dtu.dk/services/TargetP/instructions.phpGeneral10.1006/jmbi.2000.390310891285PrimaryCBSInstituteProviderHenrik Nielsenhnielsen@cbs.dtu.dkhttp://orcid.org/0000-0002-9412-9643PersonPrimary contactChloroPPrediction of presence of chloroplast transit peptides and their cleavage sites in plant proteins.http://cbs.dtu.dk/services/ChloroP/chloropbiotools:chlorop1.1Command-line toolWeb applicationhttp://edamontology.org/topic_3510Protein sites, features and motifsLinuxWindowsMacOtherMatureFree of charge (with restrictions)http://edamontology.org/operation_0422Protein cleavage site predictionhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTApredicts the presence of chloroplast transit peptides (cTP)http://www.cbs.dtu.dk/services/doc/chlorop-1.1.readmeRepositoryhttp://www.cbs.dtu.dk/services/doc/chlorop-1.1.readmeSource codehttp://www.cbs.dtu.dk/services/doc/chlorop-1.1.readmeBinarieshttp://www.cbs.dtu.dk/services/ChloroPCitation instructionshttp://www.cbs.dtu.dk/services/ChloroP/pages/instr.phpGeneral10.1110/ps.8.5.97810338008PMC2144330Primary10.1110/ps.8.5.97810338008PMC2144330OtherCBSInstituteProviderhttp://www.bioinformatics.dtu.dk/english/Service/ContactPersonPrimary contactHenrik Nielsenhnielsen@bioinformatics.dtu.dkhttp://orcid.org/0000-0002-9412-9643