Biological Language Modeling Toolkit

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Biological Language Modeling Toolkit Graphing
Utilities

• by Danny Lam

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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

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BLMT Mutual Information

• Mutual Information -gt 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 -gt
• first column is position in sequence
• second column is mutual information value
  associated with that position

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Feature Positions

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

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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.
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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.

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a1,b1textread(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
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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).

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Subplotter

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

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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
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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)?
--gt 3
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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 ...
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Subplotter (Version 1)
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Current/Future Work

• Generate graphing utility for every tool on the
  BLMT website.

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Questions?