CORRESPOND

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Table of Contents
FUNCTION
DESCRIPTION
EXAMPLE
OUTPUT
INPUT FILES
RELATED PROGRAMS
RESTRICTIONS
STATISTIC USED
SUGGESTIONS
COMMAND-LINE SUMMARY
LOCAL DATA FILES
PARAMETER REFERENCE

FUNCTION

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Correspond looks for similar patterns of codon usage by comparing codon frequency tables.

DESCRIPTION

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The frequencies compared are the number of instances of the codon in question divided by the total number of codons specifying that amino acid or terminator in each table. The statistic gets smaller as the patterns of codon usage become more similar (see Grantham, Nucl. Acids Res. 9(1); r43-r74 (1981)). Correspond requires codon frequency tables generated by CodonFrequency as the object of the comparison. If an amino acid is not used at all in one of the tables, its codons contribute nothing to the sum of squares. These ignored codons are counted and reported. You can write the results of a session with Correspond to a file or display the results on the screen only. You may use ambiguous file names or an indirect file specification (list file) to specify the input file(s), and Correspond makes all of the implied comparisons.

EXAMPLE

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Here is session using Correspond to find the correspondence among all of the files ending in .cod that are provided in the Wisconsin Package(TM):


% correspond

 Do you want to file the results (* No *) ?  Y

 What should I call the output file (* correspond.cor *) ?

 CORRESPOND of what frequency file(s) ?  *.cod

 to what other frequency file(s) (* *.cod *) ?

 /////////////////////////////////////////////

%

OUTPUT

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Correspond always writes output to your screen. You can also choose to file the results. Here is part of the output file from the example session:


 CORRESPOND  October 13, 1998 10:16

Between                       and    D-Squared   D   Not-Counted ..

ecohigh.cod           ecohigh.cod    0.000000    0.000000   3
ecohigh.cod            ecolow.cod    3.389802    1.841141   3
ecohigh.cod         ggammacod.cod    5.736563    2.395112   3

///////////////////////////////////////////////////////////////////

INPUT FILES

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Correspond accepts as input two or more codon frequency files in the same format as the files created by CodonFrequency. (Correspond reads only the fourth column of information for calculating frequencies.) The files may be specified as single file specifications or by using multiple file specifications. Acceptable multiple file specifications are an ambiguous file specification using an asterisk wildcard, for example *.cod; or a list file, for example @codontables.list.

RELATED PROGRAMS

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CodonFrequency generates codon frequency tables. CodonPreference finds regions of sequences that show a preference for a pattern of codon choices in a codon frequency table.

RESTRICTIONS

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If you use multiple file specifications, all of the files in the set of files implied by your file name or list file name must be real codon frequency tables like the ones written by CodonFrequency. If no valid files are named by either file specification, Correspond halts without doing anything.

STATISTIC USED

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Correspond reads the normalized (/1000) data from the fourth column of the codon frequency table. It then totals these figures for each synonymous family. If the total for a family in either table is 0.0, then none of the codons from that family contribute anything to the value of D squared.

Frequency((codon)) = Number((column 4)) / Total((family))

    D squared = Sum over all 64 codons of:

    ( Freq((codon,table 1)) - Frequency((codon,table 2)) ) (2)

SUGGESTIONS

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If you plan to compare many codon frequency tables, naming your tables with the extension .cod simplifies your task. This allows you to specify the files ambiguously with *.cod.

COMMAND-LINE SUMMARY

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All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.


CORRESPOND does not support complete command-line control.

Local Data Files: None

Optional Parameters:

-CONtinue     automatically prompts for the next input file after completing
                the first comparison

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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You can set the parameter listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.

-CONtinue

makes this program loop back to the beginning and prompt for more input files after the comparison is done.

Printed: December 9, 1998 16:26 (1162)

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