Random Number Generators Mutations and Randomization
7.1 Random Number Generators
A random number generator is a subroutine you can call. For most practical purposes, you neednt worry about whats inside it. The values you get for random numbers on the computer differ somewhat from the values of real-world random events as measured, for example, by detecting nuclear decay events. Some computers actually have devices such as geiger counters attached so as to have a source of truly random events. But Id be willing to bet your computer doesnt. What you have in place of a geiger counter, is an algorithm called a random number generator. The numbers that are output by random number generators are not really random; they are thus called pseudo-random numbers. A random number generator, being an algorithm, is predictable. A random number generator needs a seed, an input you can change to get a different series of pseudo-random numbers. The numbers from a random number generator give an even distribution of values. This is one of the most important characteristics of randomness and largely justifies the use of these algorithms where some amount of random behavior is desired. The other take-home message about random number generators is that the seed you start them up with should itself be selected randomly. If you seed with the same number every time, youll get the same sequence of random numbers every time as well. Not very random Try to pick a seed that has some randomness in it, such as a number calculated from some computer event that changes haphazardly over time. [1] [1] Even here, for critical applications, youre not out of the woods. Unless you pick your seeds carefully, hackers will figure out how youre picking them and crack your random numbers and therefore your passwords. The method used to generate seeds in this chapter, time| , is crackable by dedicated hackers. A better choice is time +15 . If program security is important, you should consult the Perl documentation, and the Math::Random and Math::TrulyRandom modules from CPAN In the examples that follow, I use a simple method for seed picking thats okay for most purposes. If you use random numbers for data encryption with critical privacy issues such as patient records, you should read further into the Perl documentation about the several advanced options Perl provides for random number generation. In this book, I use a Perl method that is good enough for most purposes.7.2 A Program Using Randomization
Parts
» OReilly.Beginning.Perl For Bioinformatics
» The Organization of Proteins
» In Silico Biology and Computer Science
» A Low and Long Learning Curve
» Ease of Programming Rapid Prototyping
» Portability, Speed, and Program Maintenance
» Perl May Already Be Installed No Internet Access?
» Downloading Binary Versus Source Code
» Unix and Linux Macintosh Windows
» Unix or Linux How to Run Perl Programs
» Text Editors Getting Started with Perl
» Finding Help Getting Started with Perl
» Saves and Backups Error Messages
» Individual Approaches to Programming Programming Strategies
» The Design Phase The Programming Process
» Algorithms The Programming Process
» Pseudocode and Code Comments
» Representing Sequence Data Sequences and Strings
» Control Flow Comments Revisited Command Interpretation
» Assignment Print Exit Statements
» Concatenating DNA Fragments Sequences and Strings
» Using the Perl Documentation
» Calculating the Reverse Complement in Perl
» Proteins, Files, and Arrays Reading Proteins in Files
» Arrays Sequences and Strings
» Scalar and List Context Exercises
» Conditional tests and matching braces
» Code Layout Motifs and Loops
» Getting User Input from the Keyboard Turning Arrays into Scalars with join
» Regular expressions and character classes
» Counting Nucleotides Motifs and Loops
» Exploding Strings into Arrays
» Operating on Strings Motifs and Loops
» Writing to Files Motifs and Loops
» Advantages of Subroutines Subroutines
» Arguments Scoping and Subroutines
» Scoping Scoping and Subroutines
» Command-Line Arguments and Arrays
» Subroutines: Pass by Value Subroutines: Pass by Reference
» Modules and Libraries of Subroutines
» use warnings; and use strict; Fixing Bugs with Comments and Print Statements
» How to start and stop the debugger Debugger command summary
» Stepping through statements with the debugger
» Setting breakpoints The Perl Debugger
» Fixing another bug use warnings; and use strict; redux
» Exercises Subroutines and Bugs
» Random Number Generators Mutations and Randomization
» Seeding the Random Number Generator Control Flow
» Making a Sentence Randomly Selecting an Element of an Array
» Formatting A Program Using Randomization
» Select a random position in a string Choose a random nucleotide
» Improving the Design Combining the Subroutines to Simulate Mutation
» Exercises Mutations and Randomization
» A Gene Expression Database Gene Expression Data Using Unsorted Arrays
» Gene Expression Data Using Sorted Arrays and Binary Search
» Gene Expression Data Using Hashes
» Translating Codons to Amino Acids
» The Redundancy of the Genetic Code
» Using Hashes for the Genetic Code
» Translating DNA into Proteins
» FASTA Format Reading DNA from Files in FASTA Format
» A Design to Read FASTA Files
» A Subroutine to Read FASTA Files
» Writing Formatted Sequence Data
» Regular Expressions Restriction Maps and Regular Expressions
» Background Planning the Program
» Restriction Enzyme Data Restriction Maps and Restriction Enzymes
» Logical Operators and the Range Operator
» Finding the Restriction Sites
» Exercises Restriction Maps and Regular Expressions
» Using Arrays Separating Sequence and Annotation
» Pattern modifiers Examples of pattern modifiers
» Separating annotations from sequence
» Using Arrays Parsing Annotations
» When to Use Regular Expressions
» Main Program Parsing Annotations
» Parsing Annotations at the Top Level
» Features Parsing the FEATURES Table
» Parsing Parsing the FEATURES Table
» DBM Essentials Indexing GenBank with DBM
» Overview of PDB Protein Data Bank
» Opening Directories Files and Folders
» Processing Many Files Files and Folders
» Extracting Primary Sequence Parsing PDB Files
» Finding Atomic Coordinates Parsing PDB Files
» The Stride Secondary Structure Predictor
» Parsing Stride Output Controlling Other Programs
» String Matching and Homology
» Extracting Annotation and Alignments
» Parsing BLAST Alignments Parsing BLAST Output
» The printf Function Presenting Data
» here Documents format and write
» Bioperl Tutorial Script Bioperl
» The Art of Program Design Web Programming
» Algorithms and Sequence Alignment Object-Oriented Programming Complex Data Structures
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