PPE simulates cis-regulatory sequence evolution via local point mutations, according to a variety of nucleotide substitution models.
DESCRIPTION
PPE
receives as input a string and a substring. The string represents a DNA sequence, whereas the substring represents a transcription factor binding site. During a run,
PPE
scans the string for the substring. If the substring is present, the run terminates; otherwise, a pseudorandom number generator is used to determine whether a base change will occur, according to a particular molecular evolution model and mutation rate chosen by the user (secondary base-changes also are possible). Scanning and base-changing are iterated until the substring is established.
PPE
was composed by Jonathon R. Stone and Gregory A. Wray (2001. Rapid evolution of
cis-regulatory
sequences via local point mutations. Molecular Biology and Evolution 18:1764-1770).
IMPLEMENTATION
Initially, the user is provided with three options:
1. input string from file
2. use program-generated string of psuedorandom composition
3. quit
If options 1 or 2 are selected, then the user is prompted to enter a nucleotide substitution model (standing distribution, one-parameter, two-parameter, or general), one or more
mutation rates, a text file name containing a string (option 1) or a string length (option 2), a substring, and a filename path on which to record output.
OUTPUT
The program returns a variety of data
(e.g.,
iterations transpired -- generations required) for subsequent analysis.
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To obtain additional information concerning
PPE
, please feel welcome to email