Mercurial > repos > bioinformatics_lab_ufsc > epibuilder
view test-data/command-epifinder.txt @ 5:37946f736ac9 draft
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| author | bioinformatics_lab_ufsc |
|---|---|
| date | Thu, 25 Nov 2021 04:25:33 +0000 |
| parents | ef26009cd70a |
| children |
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---- Running Parameters ---- BepiPred-2.0 Threshold : 0.6 Min epitope length : 10 Max epitope length : 30 ---- Softwares Threshold ---- Emini : 0.8 Parker : 0.8 Chou Fosman : 0.8 Karplus Schulz : 0.8 Kolaskar : 0.8 ---- Proteomes ---- Alias File test_proteom /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta ---- Blast ---- Identity : 90.0 Cover : 90.0 Word size : 4 Task blastp-short: blastp-short ---- Stats ---- Processed proteins : 6 NGlycosylated proteins : 0 Identified epitopes : 3 N-glycosylated epitopes: 0 ---- Protein Summary ---- Id Epitopes N-Glyc 5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta 0 0 4XAK_A Chain A of Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD 0 0 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation 1 0 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 0 5C0N_A Chain A of Development of a therapeutic monoclonal antibody that targets secreted fatty acid-binding protein aP2 to treat type 2 diabetes. 0 0 4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2 0 0 ---- Epitopes list ---- N Id Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length MW(kDa) I.P Hydropathy All Matches Cover Avg Cover BepiPred2 Emini Parker Chou Fosman Karplus Schulz Kolaskar test_proteom_count test_proteom_acc test_proteom_count test_proteom_id 1 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation PETQSSHSAW 73 83 N 0 - 10 1.13 5.25 -1.40 0.90 0.98 0.65 2.57 4.19 1.13 1.04 0.99 1 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 1 4WFF_B(100.00,100.00) 2 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation AIFLKWHVPPELVR 149 163 N 0 - 14 1.71 8.80 0.42 0.07 0.60 0.64 0.82 -1.83 0.83 0.96 1.10 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00) 3 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation LKWHVPPELVRVLSA 150 165 N 0 - 15 1.74 8.75 0.39 0.07 0.59 0.63 0.81 -1.70 0.84 0.96 1.11 2 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation,4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 4WFF_B(100.00,100.00),4WFF_A(100.00,100.00) ---- Epitopes topology ---- N Id Method Threshold Avg Score Cover Epitope Start End N-Glyc N-Glyc-Count N-Glyc-Motifs Length kDa I.P Avg Hydropathy Avg Cover 1 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation BepiPred-2.0 0.60 0.65 - PETQSSHSAW 73 83 N 0 - 10 1.13 5.25 -1.40 0.98 Emini 0.80 2.57 0.90 EEEEEEEEE. Parker 0.80 4.19 1.00 EEEEEEEEEE Chou Fosman 0.80 1.13 1.00 EEEEEEEEEE Karplus Schulz 0.80 1.04 1.00 EEEEEEEEEE Kolaskar 0.80 0.99 1.00 EEEEEEEEEE All matches - - 0.90 EEEEEEEEE. N-Glyc - - - .......... Hydropathy - -1.40 - --------+- 2 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation BepiPred-2.0 0.60 0.64 - AIFLKWHVPPELVR 149 163 N 0 - 14 1.71 8.80 0.42 0.60 Emini 0.80 0.82 0.43 .....EEEE.EE.. Parker 0.80 -1.83 0.07 .......E...... Chou Fosman 0.80 0.83 0.50 .....EEEEEEE.. Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEE Kolaskar 0.80 1.10 1.00 EEEEEEEEEEEEEE All matches - - 0.07 .......E...... N-Glyc - - - .............. Hydropathy - 0.42 - ++++---+---++- 3 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation BepiPred-2.0 0.60 0.63 - LKWHVPPELVRVLSA 150 165 N 0 - 15 1.74 8.75 0.39 0.59 Emini 0.80 0.81 0.40 ..EEEE.EE...... Parker 0.80 -1.70 0.07 ....E.......... Chou Fosman 0.80 0.84 0.47 ..EEEEEEE...... Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEEE Kolaskar 0.80 1.11 1.00 EEEEEEEEEEEEEEE All matches - - 0.07 ....E.......... N-Glyc - - - ............... Hydropathy - 0.39 - +---+---++-++-+ Generated files: ./command-epifinder-parameters.txt ./command-epifinder-protein-summary.tsv ./command-epifinder-topology.tsv ./command-epifinder-epitope-detail.tsv ./command-epifinder-scores.tsv ./command-epifinder-epitopes-fasta.fasta