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Biological Language Modeling Toolkit “Graphing Utilities”

Biological Language Modeling Toolkit “Graphing Utilities”. by: Danny Lam. Overview. BLMT Ex : Computes association measures in protein sequences Graphing Utilities Display how well the association measures or other data ( known or surmised ) feature boundaries

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Biological Language Modeling Toolkit “Graphing Utilities”

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  1. Biological Language Modeling Toolkit“Graphing Utilities” by: Danny Lam

  2. Overview • BLMT Ex: Computes association measures in protein sequences • Graphing Utilities • Display how well the association measures or other data (known or surmised) feature boundaries • Step 1: Automatic extraction of feature boundaries from given source files • Step 2: Plot data along with feature positions along a sequence

  3. BLMT : Mutual Information • Mutual Information-> Computes "mutual information”, which is a measure of association between adjacent amino acids. • Input: amino acid sequence file(s) • (ex) Swiss prot SW datasets • Output: file.mi.out.av -> • first column is position in sequence • second column is mutual information value associated with that position

  4. Feature Positions • Extract feature position information (via Swiss-prot) • Extracellular (EC), • Cytoplasmic (CP), • Helices (H) --> label where the EC, CP, and H regions are in the sequence.

  5. DR PROSITE; PS00238; OPSIN; 1. KW Photoreceptor; Retinal protein; Transmembrane; Glycoprotein; Vision; KW Phosphorylation; Lipoprotein; Palmitate; G-protein coupled receptor; KW Acetylation; Retinitis pigmentosa; Disease mutation. FT DOMAIN 1 36 EXTRACELLULAR. FT TRANSMEM 37 61 1 (POTENTIAL). FT DOMAIN 62 73 CYTOPLASMIC. FT TRANSMEM 74 98 2 (POTENTIAL). FT DOMAIN 99 113 EXTRACELLULAR. FT TRANSMEM 114 133 3 (POTENTIAL). FT DOMAIN 134 152 CYTOPLASMIC. FT TRANSMEM 153 176 4 (POTENTIAL). FT DOMAIN 177 202 EXTRACELLULAR. FT TRANSMEM 203 230 5 (POTENTIAL). FT DOMAIN 231 252 CYTOPLASMIC. FT TRANSMEM 253 276 6 (POTENTIAL). FT DOMAIN 277 284 EXTRACELLULAR. FT TRANSMEM 285 309 7 (POTENTIAL). FT DOMAIN 310 348 CYTOPLASMIC. FT MOD_RES 1 1 ACETYLATION (BY SIMILARITY). FT CARBOHYD 2 2 N-LINKED (GLCNAC...) (BY SIMILARITY). FT CARBOHYD 15 15 N-LINKED (GLCNAC...) (BY SIMILARITY). FT DISULFID 110 187 BY SIMILARITY. FT BINDING 296 296 RETINAL CHROMOPHORE.

  6. Problems/Solution • Problems: -Making one subplot graph (MATLAB) requires program customization - Generation of multiple subplots together requires more tedious work. Waste of time and effort. • Solution: -Need clear interface to generate subplot graphs for you w/o writing tedious matlab code.

  7. [a1,b1]=textread(’test.out', '%d %f'); hold on subplot(1,1,1); hold on hh1 = plot(a1, b1, 'linewidth',2.5); hold on ylabel('yaxis','fontsize',16, 'Color','k','fontweight','bold'); set(hh1, 'MarkerSize',5); set(gca, 'YLim',[-1, 3]); %set(gca,'ytick',[-.6,-.2,.2] xdash = [NaN,62,73,NaN,134,152,NaN,231,252,NaN,310,348]; %cp ydash = (-.2)*(ones(size(xdash))); line(xdash,ydash,'color','y','linewidth',3); xdash = [1,36,NaN,99,113,NaN,177,202,NaN,277,284,NaN]; %ec ydash = (-.2)*(ones(size(xdash))); line(xdash,ydash,'color','r','linewidth',3); hold on xlabel('x_axis','fontsize',16, 'Color','k'); print -dpsc -r0 sample;

  8. Design Capabilities • Access multiple mutual information output datasets • Display combination of EC/CP/H position information on MI datasets (color coded) • Specify range (Y limits) and naming conventions (X axis) • Output into convenient picture files (ex: .tiff file).

  9. Subplotter • Version 1: (In house use only) -Initially the program takes as input: --> .SW file: (EC/CP/H) --> .m file: (MATLAB file that code will be generated in)

  10. Subplotter ( Version 1) *********************************** How many output files to textread: 1 What is the file to be textread into matlab program [output file 1]: opsdh_1gpcr.out How many TOTAL subplots do you request?: 1 ************************************

  11. Subplotter ( Version 1) ********************* Subplot(1,1,1) ********************* Which file do you want results to be graphed on this subplot?: 0: opsdh_1gpcr.out Make selection (0): 0 ++++++++++++++++++++++++++++++++++++++++++++++ How many items (EC,CP,H) do you want plotted (1,2, 3: GPCR, 4: Loops)?: +++++++++++++++++++++++++++++++++++++++++++++++ --> 3

  12. Subplotter ( Version 1) Specify Y-Axis Label? (y/n): n Y-Axis Label: GPCR Specify YLim? (y,n): n Give name to X-Axis: sample Give name to .tiff file for output (no extension!): sample Matlab Program completed! wait ...

  13. Subplotter (Version 1)

  14. Current/Future Work • Generate graphing utility for every tool on the BLMT website.

  15. Questions?

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