Delila Program: gedo

gedo program

Documentation for the gedo program is below, with links to related programs in the "see also" section.

{   version = 1.08; (* of gedo.p 2015 May 12}

(* begin module describe.gedo *)
(*
name
   gedo: gene dosage

synopsis
   gedo(gedop: in, result: out, output: out)

files

   result:  results in a table computed according to
      Condon.Squires1993

   gedop:  parameters to control the program.  The file must contain the
      following parameters, one per line:

      parameterversion: The version number of the program.  This allows the
         user to be warned if an old parameter file is used.

      line 2: width and decimal places of output

      line 3: doubling time in minutes

      line 4: OriC minutes of a locus on the E. coli map

      remaining lines(real, string):
        minutes of locus
        name
      If a line begins with '*' then it is a comment line
      and is skipped.
      If a line begins with 'n' then it is calculated and
      shown but not incuded in the sum calculation.

   output: messages to the user

description

   Compute gene dosage in E. coli based on chromosome location of a
   locus, location of the origin and doubling time.

examples

In Condon.Squires1993
page 1411 is the example:

    "A wildtype E. coli strain with a doubling time of 24.1 min has an
    equivalent of 38 rRNA operons, due to the high replication rate on
    rich media (for calculation, see Materials and methods).

There is only a minor a discrepancy between this result (38) and the
following (36).

Example gedop from the Condon.Squires1993:

1.00 version of gedo that this parameter file is designed for.
6 3  width and decimal places of output
24.1 doubling time in minutes
  84.0 OriC minutes of a locus on the E. coli map
  84.5 rrnC
  86.5 rrnA
  89.8 rrnB
  90.5 rrnE
  05.1 rrnH
  56.1 rrnG
  72.1 rrnD
n 17.5 lambda att

result file:

gedo 1.02
24.1 doubling time (min)
84.0 OriC minutes of a locus on the E. coli map
 1.73 the specific growth rate in $h^{-1}$
   min      f      D      C      x  name
84.500  0.010 23.318 42.011  6.468  rrnC
86.500  0.050 23.318 42.011  6.163  rrnA
89.800  0.116 23.318 42.011  5.690  rrnB
90.500  0.130 23.318 42.011  5.595  rrnE
 5.100  0.422 23.318 42.011  3.932  rrnH
56.100  0.558 23.318 42.011  3.336  rrnG
72.100  0.238 23.318 42.011  4.910  rrnD
17.500  0.670 23.318 42.011  2.914  lambda att - skipped in sum
36.094 sum of x

documentation

See pages 4311 and 4314 of:

@article{Condon.Squires1993,
author = "C. Condon
 and S. French
 and C. Squires
 and C. L. Squires",
title = "{Depletion of functional ribosomal RNA operons in
\emph{Escherichia coli} causes increased expression of the remaining
intact copies}",
journal = "EMBO J",
volume = "12",
pages = "4305--4315",
pmid = "8223440",
pmcid = "PMC413727",
year = "1993"}

The equations come from Table 5, page 1538:

Bremer,H. and Dennis,P.P. (1987) In Neidhardt,F.C, Ingraham,J.L.,
Low,K.B., Magasanik,B., Schaechter,M. and Umbarger,H.E. (eds) ,
Escherichia coli and Salmonella typhimuriurn: Cellular and Molecular
Biology. American Society for Microbiology, Washington, DC, pp.
1527-1542.

see also

  Example parameter file:  gedop

author

   Thomas Dana Schneider

bugs

technical notes

*)
(* end module describe.gedo *)
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