Meltplot

• MELTPLOT(+)
  • FUNCTION
  • DESCRIPTION
  • AUTHOR
  • EXAMPLE
  • OUTPUT
  • RELATED PROGRAMS
  • RESTRICTIONS
  • ALGORITHM
  • INPUT FILE
  • GRAPHICS
  • CTRL-C
  • COMMAND-LINE SUMMARY
  • LOCAL DATA FILES
  • OPTIONAL PARAMETERS
    • -PRODuct
    • -TEMP
    • -FORMamide
    • -MISmatch
    • -TITLEText
    • -NOTITle
    • -FIGure
    • -FONT
    • -COLor
    • -SCAle
    • -XPAN
    • -YPAN
    • -PORtrait
  • REFERENCES

MELTPLOT(+)

FUNCTION

MeltPlot plots the melting curve for a nucleic acid sequence using the algorithms described by Breslauer et al. Proc. Natl. Acad. Sci. USA 83, 3746-3750 and Baldino et al. Methods in Enzymol. 168, 761-777.

DESCRIPTION

MeltPlot produces plots of Melting temperature and %C + %G profiles of a nucleic acid sequence. For the Melting temperature profile free energy values calculated from nearest neighbor thermodynamics are used (Breslauer et al. Proc. Natl. Acad. Scien. USA 83, 3746-3750, Baldino et al. Meth. Enzymol. 168, 761-777).

AUTHOR

This program was written by Rodrigo Lopez S. (E-mail: rodrigol@biotek.uio.no; Post: Biotechnology Centre of Oslo, PO Box 1125 Blindern, N-0317 Oslo 3, Norway).

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

EXAMPLE

Here is a session with MeltPlot that was used to produce the melting temperature profile for the first 1000 bases of human low density lipoprotein receptor (GenEMBL:hsldlr), using a window of 20 bases, and a shift of one.

  
  
  % meltplot
  
    MeltPlot of what nucleotide sequence  ?  GenEMBL:Hsldlr
  
              Start (* 1 *) ?
             End (* 5095 *) ? 1000
  
    What window size   (* 100 *)? 20
  
    What shift increment (* 1 *)?
  
    The minimum density for a one-page plot is 869.6 Bases/100 platen units.
    What density do you want (* 869.6 *) ?
  
  %
  

OUTPUT

This is the plot from the example session

RELATED PROGRAMS

Melt is a program that produces a text file containing the Tm and %CG profiles.

RESTRICTIONS

None

ALGORITHM

MeltPlot uses a running window of specified length on which it calculates the melting temperature and the %CG contents.

INPUT FILE

The input file for MeltPlot is a GCG formatted nucleic acid sequence.

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: % meltplot [-INfile=]GenEMBL:hsldlr -Default
  
  Prompted Parameters:
  
  -BEGin=1 -END=1000    the range of interest
  -WINdow=100           the window length
  -SHIFT=1              the window shift
  
  Local Data Files: None
  
  Optional Parameters:
  
  -PRODuct              prompts for the following values:
  
  -TEMp=55.0            minimum temperature
  -FORMamide=0.0        formamide concentration (percent)
  -MISmatch=0.0         percent mismatch
  
  Most EGCG graphics programs accept these and other switches. See the Using
  Graphics chapter of the EGCG USERS GUIDE for descriptions.
  
  -DENSity=150.0        plot density in bases per 100 platen units
  -LEFTMARgin=10.0      sets the left plot margin position
  -RIGHTMARgin=140.0    sets the right plot margin position
  -BOTTOMMARgin=10.0    sets the bottom plot margin position
  -TOPMARgin=90.0       sets the top plot margin position
  -BORDer               puts a line border around the plot
  -NOBORDer             suppresses a line border
  -PAGENUMber           forces page numbering
  -NOPAGENUMber         suppresses page numbering
  -TITletext="text"     overrides the default plot title
  -NOTITletext          suppresses the plot title
  -SUBTITletext="text"  overrides the default plot subtitle
  -NOSUBTITletext       suppresses the plot subtitle
  -CHEIGHT=1.5          default plot character height
  -LINESTyle1=1         plot line style 1 (set for each line)
  -LINEPERiod1=1        plot line period 1 (set for each line)
  -LINECOLor1=0         plot line colour 1 (set for each line)
  All GCG graphics programs accept these and other switches. See the Using
  Graphics chapter of the USERS GUIDE for descriptions.
  
  -FIGure[=FileName]  stores plot in a file for later input to FIGURE
  -FONT=3             draws all text on the plot using font 3
  -COLor=1            draws entire plot with pen in stall 1
  -SCAle=1.2          enlarges the plot by 20 percent (zoom in)
  -XPAN=10.0          moves plot to the right 10 platen units (pan right)
  -YPAN=10.0          moves plot up 10 platen units (pan up)
  -PORtrait           rotates plot 90 degrees
  

LOCAL DATA FILES

The files described below supply auxiliary data to this program. The program automatically reads them from a public data directory unless you either 1) have a data file with exactly the same name in your current working directory; or 2) name a file on the command line with an expression like -DATa1=myfile.dat. For more information see Chapter 4, Using Data Files in the User's Guide.

If you are studying a sequence with known features, this program marks the plot with small boxes showing the positions of these features. The presence of a file in your directory with the same name as your sequence and the file name extension .mrk causes the program to mark each range specified in the file. You can provide a marking file on the command line with an expression like -MARk=hsldlr.mrk. The file gamma.mrk contains information about the format of marking files. The figure for the example session shows marked regions.

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.

-PRODuct

prompts for the following three values (unless they are already specified on the command line).

-TEMP=55.0

specifies the required melting temperature.

-FORMamide=0.0

specifies the percent formamide concentration.

-MISmatch=0.0

specifies the allowed percent mismatch

-TITLEText="A Title

specifies an alternative title for the plot.

-NOTITle

suppresses the plot title

These options apply to all GCG graphics programs. These and many others are described in detail in Chapter 5, Using Graphics of the User's Guide.

-FIGure=programname.figure

writes the plot as a text file of plotting instructions suitable for input to the Figure program instead of drawing the plot on your plotter.

-FONT=3

draws all text characters on the plot using Font 3 (see Appendix I) .

-COLor=1

draws the entire plot with the pen in stall 1.

These options let you expand or reduce the plot (zoom), move it in either direction (pan), or rotate it 90 degrees (rotate).

-SCAle=1.2

expands the plot by 20 percent by resetting the scaling factor (normally 1.0) to 1.2 (zoom in). You can expand the axes independently with -XSCAle and -YSCAle. Numbers less than 1.0 contract the plot (zoom out).

-XPAN=30.0

moves the plot to the right by 30 platen units (pan right).

-YPAN=30.0

moves the plot up by 30 platen units (pan up).

-PORtrait

rotates the plot 90 degrees. Usually, plots are displayed with the horizontal axis longer than the vertical (landscape). Note that plots are reduced or enlarged, depending on the platen size, to fill the page.

REFERENCES

Breslauer, K.J., Frank, R., Blocker, H., and Marky, L.A. (1986). "Predicting DNA Duplex Stability from the Base Sequence." Proceedings of the National Academy of Sciences USA 83, 3746-3750.

Baldino, M., Jr. (1989). "High Resolution In Situ Hybridization Histochemistry." In Methods in Enzymology, (P.M. Conn, ed.), 168, 761-777, Academic Press, San Diego, California, USA.

Printed: April 22, 1996 15:54 (1162)