Mercurial > repos > bioinformatics_lab_ufsc > epibuilder
comparison test-data/command-epifinder.txt @ 0:ef26009cd70a draft
Uploaded version 1.1
| author | bioinformatics_lab_ufsc |
|---|---|
| date | Thu, 25 Nov 2021 01:26:36 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:ef26009cd70a |
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| 1 | |
| 2 ---- Running Parameters ---- | |
| 3 BepiPred-2.0 Threshold : 0.6 | |
| 4 Min epitope length : 10 | |
| 5 Max epitope length : 30 | |
| 6 | |
| 7 ---- Softwares Threshold ---- | |
| 8 Emini : 0.8 | |
| 9 Parker : 0.8 | |
| 10 Chou Fosman : 0.8 | |
| 11 Karplus Schulz : 0.8 | |
| 12 Kolaskar : 0.8 | |
| 13 | |
| 14 ---- Proteomes ---- | |
| 15 Alias File | |
| 16 test_proteom /usr/local/bioinfo/stingrayGalaxy/tools/stingray/epifinder/test-data/proteom.fasta | |
| 17 | |
| 18 ---- Blast ---- | |
| 19 Identity : 90.0 | |
| 20 Cover : 90.0 | |
| 21 Word size : 4 | |
| 22 Task blastp-short: blastp-short | |
| 23 | |
| 24 ---- Stats ---- | |
| 25 Processed proteins : 6 | |
| 26 NGlycosylated proteins : 0 | |
| 27 Identified epitopes : 3 | |
| 28 N-glycosylated epitopes: 0 | |
| 29 | |
| 30 ---- Protein Summary ---- | |
| 31 Id Epitopes N-Glyc | |
| 32 5BVP_A Chain A of The molecular mode of action and species specificity of canakinumab, a human monoclonal antibody neutralizing IL-1beta 0 0 | |
| 33 4XAK_A Chain A of Crystal structure of potent neutralizing antibody m336 in complex with MERS Co-V RBD 0 0 | |
| 34 4WFF_A Chain A of Human TRAAK K+ channel in a K+ bound nonconductive conformation 1 0 | |
| 35 4WFF_B Chain B of Human TRAAK K+ channel in a K+ bound nonconductive conformation 2 0 | |
| 36 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 | |
| 37 4Z5R_A Chain A of Rontalizumab Fab bound to Interferon-a2 0 0 | |
| 38 | |
| 39 ---- Epitopes list ---- | |
| 40 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 | |
| 41 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) | |
| 42 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) | |
| 43 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) | |
| 44 | |
| 45 ---- Epitopes topology ---- | |
| 46 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 | |
| 47 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 | |
| 48 Emini 0.80 2.57 0.90 EEEEEEEEE. | |
| 49 Parker 0.80 4.19 1.00 EEEEEEEEEE | |
| 50 Chou Fosman 0.80 1.13 1.00 EEEEEEEEEE | |
| 51 Karplus Schulz 0.80 1.04 1.00 EEEEEEEEEE | |
| 52 Kolaskar 0.80 0.99 1.00 EEEEEEEEEE | |
| 53 All matches - - 0.90 EEEEEEEEE. | |
| 54 N-Glyc - - - .......... | |
| 55 Hydropathy - -1.40 - --------+- | |
| 56 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 | |
| 57 Emini 0.80 0.82 0.43 .....EEEE.EE.. | |
| 58 Parker 0.80 -1.83 0.07 .......E...... | |
| 59 Chou Fosman 0.80 0.83 0.50 .....EEEEEEE.. | |
| 60 Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEE | |
| 61 Kolaskar 0.80 1.10 1.00 EEEEEEEEEEEEEE | |
| 62 All matches - - 0.07 .......E...... | |
| 63 N-Glyc - - - .............. | |
| 64 Hydropathy - 0.42 - ++++---+---++- | |
| 65 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 | |
| 66 Emini 0.80 0.81 0.40 ..EEEE.EE...... | |
| 67 Parker 0.80 -1.70 0.07 ....E.......... | |
| 68 Chou Fosman 0.80 0.84 0.47 ..EEEEEEE...... | |
| 69 Karplus Schulz 0.80 0.96 1.00 EEEEEEEEEEEEEEE | |
| 70 Kolaskar 0.80 1.11 1.00 EEEEEEEEEEEEEEE | |
| 71 All matches - - 0.07 ....E.......... | |
| 72 N-Glyc - - - ............... | |
| 73 Hydropathy - 0.39 - +---+---++-++-+ | |
| 74 Generated files: | |
| 75 ./command-epifinder-parameters.txt | |
| 76 ./command-epifinder-protein-summary.tsv | |
| 77 ./command-epifinder-topology.tsv | |
| 78 ./command-epifinder-epitope-detail.tsv | |
| 79 ./command-epifinder-scores.tsv | |
| 80 ./command-epifinder-epitopes-fasta.fasta |