Mercurial > repos > bioinformatics_lab_ufsc > epibuilder
diff test-data/command-epifinder.txt @ 0:ef26009cd70a draft
Uploaded version 1.1
| author | bioinformatics_lab_ufsc |
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| date | Thu, 25 Nov 2021 01:26:36 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/command-epifinder.txt Thu Nov 25 01:26:36 2021 +0000 @@ -0,0 +1,80 @@ + +---- 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 \ No newline at end of file