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