Gene finding and splice sites | Description | 简介 |
EasyGene | Gene finding in prokaryotes | 原核生物中的基因发现 |
HMMgene | Prediction of vertebrate and C. elegans genes | 脊椎动物和秀丽隐杆线虫基因的预测 |
NetAspGene | Intron splice sites in Aspergillus DNA | 曲霉菌DNA中的内含子剪接位点 |
NetGene2 | Intron splice sites in human, C. elegans and A. thaliana DNA | 人、秀丽隐杆线虫和拟南芥DNA中的内含子剪接位点 |
NetStart | Translation start in vertebrate and A. thaliana DNA | 脊椎动物和拟南芥DNA的翻译开始 |
NetUTR | Splice sites in 5' UTR regions of human genes | 人类基因5'UTR区的剪接位点 |
Promoter | Transcription start sites in vertebrate DNA | 脊椎动物DNA中的转录起始位点 |
Genomic epidemiology |
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CSI Phylogeny | CSI Phylogeny calls SNPs, filters the SNPs, does site validation and infers a phylogeny | CSI系统发育调用SNPs，过滤SNPs，进行位点验证并推断系统发育 |
KmerFinder | Prediction of bacterial species using a fast K-mer algorithm | 利用快速K-mer算法预测细菌种类 |
MLST | Multi Locus Sequence Typing (MLST) from an assembled genome or from a set of reads | 从组装的基因组或一组读数进行多位点序列分型（MLST） |
Ndtree | NDtreePhylogenic tree from reads using nucleotide difference method | NDtree使用核苷酸差异法读取的系统发育树 |
PathogenFinder | Prediction of a bacteria's pathogenicity towards human hosts | 细菌对人类宿主致病性的预测 |
ResFinder | Identifcation of acquired antibiotic resistance genes | 获得性抗生素耐药性基因的鉴定 |
Immunological features |
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ArrayPitope | Residue-level epitope mapping of antigens based on peptide microarray data | 基于肽微阵列数据的抗原残基水平表位定位 |
BepiPred | Prediction of potential B-cell epitopes from protein sequence | 从蛋白质序列预测潜在的B细胞表位 |
DiscoTope | Improved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations | 使用AlphaFold2建模和反向折叠潜在表示改进的B细胞表位预测 |
LYRA | Lymphocyte receptor automated modelling | 淋巴细胞受体自动化建模 |
MAIT Match | Calculate similarity between CDR3 sequences and a reference database of MAIT sequences | 计算CDR3序列与MAIT序列参考数据库之间的相似性 |
MHCMotifDecon | Motif deconvolution of Multi-allele immunopetidomics data | 多等位基因免疫组学数据的Motif反褶积 |
MHCcluster | MHC clustring based on binding specififcity | 基于绑定特定性的MHC集群字符串 |
MuPeXI | Prediction of neo-epitopes from tumor sequencing data | 从肿瘤测序数据预测新表位 |
NNAlign | Discovering sequence motifs in biological sequences | 发现生物序列中的序列基序 |
NetAllergen | Protein allergenicity prediction | 蛋白质致敏性预测 |
NetBoLAIIpan | Prediction of peptide interactions with bovine MHC Class II BoLA-DRB3 molecules | 肽与牛MHC II类BoLA-DRB3分子相互作用的预测 |
NetCTL | Predection of CTL epitopes in protein sequences | 蛋白质序列中CTL表位的预测 |
NetCTLpan | Pan-specific integrated class I antigen presentation | 泛特异性整合I类抗原呈递 |
NetChop | Proteasomal cleavages (MHC ligands) | 蛋白酶体裂解（MHC配体） |
NetH2pan | Prediction of peptide interactions with murine MHC class I (H2) molecules. | 肽与鼠MHC I类（H2）分子相互作用的预测。 |
NetMHC | NetMHC: Binding of peptides to MHC class I molecules | NetMHC：肽与MHC I类分子的结合 |
NetMHCII | Binding of peptides to MHC class II molecules | 肽与MHC II类分子的结合 |
NetMHCIIpan | Pan-specific binding of peptides to MHC class II molecules of known sequence | 肽与已知序列的MHC II类分子的泛特异性结合 |
NetMHCcons | Binding of peptides to any known MHC class I molecule | 肽与任何已知MHC I类分子的结合 |
NetMHCpan | Pan-specific binding of peptides to MHC class I proteins of known sequence | 肽与已知序列的MHC I类蛋白的泛特异性结合 |
NetMHCpanExp | Pan-specific binding of peptides to MHC class I proteins of known sequence including antigen expression | 肽与包括抗原表达在内的已知序列的MHC I类蛋白的泛特异性结合 |
NetMHCphosPan | Pan-specific binding of phosphorylated peptides to HLA class I molecules. | 磷酸化肽与HLA I类分子的泛特异性结合。 |
NetMHCstabpan | Pan-specific stability of peptide:MHC-I complexes | 肽的泛特异性稳定性：MHC-I复合物 |
NetPolyEV | Construction of Polytope Vaccines | 多聚体疫苗的构建 |
NetTCR | Sequence-based prediction of peptide-TCR binding. | 基于序列的肽TCR结合预测。 |
NetTepi | T-cell epitopes restricted to prevalent HLA-A and HLA-B molecules | 仅限于流行的HLA-A和HLA-B分子的T细胞表位 |
PickPocket | Binding of peptides to any known MHC class I molecule using binding pocket matrix extrapolation | 使用结合口袋基质外推法将肽与任何已知的MHC I类分子结合 |
PopCover | Selection of MHC epitopes for optimal population and pathogen coverage | MHC表位的选择以获得最佳群体和病原体覆盖率 |
TCRbaseg. | Sequence similarity-based prediction of peptide-TCR bindin | 基于序列相似性的肽TCR结合蛋白预测 |
TCRpMHCmodels | Structural modeling tool of TCR-pMHC class I complexes | TCR-pMHC I类配合物的结构建模工具 |
VDJSolver | Analysis of human immunoglobulin VDJ recombination | 人免疫球蛋白VDJ重组分析 |
Post-translational modifications of proteins |
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DictyOGlyc | O-(alpha)-GlcNAc glycosylation sites (trained on Dictyostelium discoideum proteins) | O-（α）-GlcNAc糖基化位点（在盘基网柄菌蛋白质上训练） |
NetCGlyc | C-mannosylation sites in mammalian proteins | 哺乳动物蛋白质中的C-甘露糖基化位点 |
NetCorona | Coronavirus 3C-like proteinase cleavage sites in proteins | 蛋白质中的冠状病毒3C样蛋白酶切割位点 |
NetGPI | GPI Anchor predictions | GPI锚点预测 |
NetNGlyc | N-linked glycosylation sites in human proteins | 人类蛋白质中的N-连接糖基化位点 |
NetOGlyc | O-GalNAc (mucin type) glycosylation sites in mammalian proteins | 哺乳动物蛋白质中的O-GalNAc（粘蛋白型）糖基化位点 |
NetPhos | Generic phosphorylation sites in eukaryotic proteins | 真核蛋白质中的通用磷酸化位点 |
NetPhosBac | Generic phosphorylation sites in bacterial proteins | 细菌蛋白质中的通用磷酸化位点 |
NetPhosYeast | Serine and threonine phosphorylation sites in yeast proteins | 酵母蛋白中的丝氨酸和苏氨酸磷酸化位点 |
NetPhospan | Prediction of phosphorylation using convolutional neural networks (CNNs). | 使用卷积神经网络（CNNs）预测磷酸化。 |
NetworKIN | In vivo kinase-substrate relationships | 体内激酶与底物的关系 |
ProP | Arginine and lysine propeptide cleavage sites in eukaryotic protein sequences | 真核蛋白质序列中的精氨酸和赖氨酸前肽切割位点 |
