Profileplot

• PROFILEPLOT(+)
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • INPUT FILE
  • CALCULATING FREQUENCY
  • PLOTTING FREQUENCY
  • GRAPHICS
  • CTRL-C
  • COMMAND-LINE SUMMARY
  • OPTIONAL PARAMETERS
    • -WINdow
    • -SHIft
    • -LIMit
    • -MISmatch
    • -PROtein

PROFILEPLOT(+)

FUNCTION

ProfilePlot produces a graphical report of the frequency of patterns in a protein or nucleotide sequence.

DESCRIPTION

ProfilePlot plots the "frequency" of patterns (possibly defined using regular expressions) in a sequence (possibly a peptide one). Up to four patterns can be displayed simultaneously.

AUTHOR

This program was written by Philippe Dessen (E-mail: dessen@infobiogen.fr) and colleagues at the French EMBnet node (Post: INFOBIOGEN, 7 rue Guy Moquet - BP8, 94801 Villejuif CEDEX, France).

All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).

EXAMPLE

Here is a sample session with ProfilePlot

  
  
  % profileplot -lim -win=100 -shi=2
  
   PROFILEPLOT uses any sequence data
  
   PROFILEPLOT of what sequence: ? GenEMBL:hsmyopka
  
  
   Pattern 1: (AT){1,}
   Lower limit (* 0 *):
   Upper Limit (* 1 *): 0.2
  
   Pattern 2: T(AA,GA,AG)
   Lower limit (* 0 *):
   Upper Limit (* 1 *): 0.2
  
   Pattern 3: CG
   Lower limit (* 0 *):
   Upper Limit (* 1 *): 0.4
  
   Pattern 4:  ?
  
   PostScript instructions for a LASERWRITER are now being sent to gcgplot.ps.
  %
  

OUTPUT

This is the plot from the example session

INPUT FILE

The input file of ProfilePlot is a GCG formatted nucleic acid or peptide sequence.

CALCULATING FREQUENCY

ProfilePlot calculates frequencies over a window. This window can be defined using the qualifiers -WINdow (setting the window size) and -SHIft setting the shift increment used to move the window over the sequence within its range of interest).

The search for patterns matching the regular expresssion in the window begins at the first base of the window. If there is no match, the search restarts on the next base. If several matches are found the shorter is chosen (because several patterns can match a single regular expression). Its length is added to the counter of occurrence then the search restarts at the end of the found pattern. When the end of the window is reached, the counter of occurrence is divided by the window size which gives as a result the frequency.

PLOTTING FREQUENCY

Each pattern has its own graph. The graphic window is divided relatively to their number. If you specified the -LIMit command-line parameter, the limits of the frequency scale will be asked during the pattern specification (as shown in the example), allowing you to have a more precise view for rare patterns.

GRAPHICS

The Wisconsin Package must be configured for graphics before you run any program with graphics output! If the % setplot command is available in your installation, this is the easiest way to establish your graphics configuration, but you can also use commands like % postscript that correspond to the graphics languages the Wisconsin Package supports. See Chapter 5, Using Graphics in the User's Guide for more information about configuring your process for graphics.

CTRL-C

If you need to stop this program, use C to reset your terminal and session as gracefully as possible. Searches and comparisons write out the results from the part of the search that is complete when you use C. The graphics device should stop plotting the current page and start plotting the next page. If the current page is the last page, plotters should put the pen away and graphic terminals should return to interactive mode.

COMMAND-LINE SUMMARY

All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

  
  
  Minimum Syntax: % profileplot [-INfile=]gb_pr:hummyopka -Default
  
  Prompted Parameters:
  
  -BEGin=1   -END=500     the range of interest
  -WINdow=50              the window length
  -SHIft=1                the window shift
  -LIMit                  allows changing scale
  -MISmatch=0             allowed mismatches during pattern recognition
  -PROtein                treats the sequence as peptide
  
  Local Data Files: None
  
  Optional Parameters: None
  

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

-WINdow=50

Specifies the window size.

-SHIft=1

Specifies the shift increment (used to move the window over the sequence).

-LIMit

Allows the specification of a frequency scale for each pattern.

-MISmatch=0

Allows mismatches during pattern recognition (careful use recommended!).

-PROtein=0

Forces the program to treat the sequence as a peptide.