C

C, The Organization of DNA (see cytosine)

c (continue) command, Setting breakpoints

C compiler for Perl source code, Unix and Linux

calling, Subroutines, Advantages of Subroutines, Subroutines: Pass by Value, use warnings; and use strict;, Parsing BLAST Alignments

Perl interpreter from command line, use warnings; and use strict;

subroutine arguments by reference, Parsing BLAST Alignments

subroutine arguments by value, Subroutines: Pass by Value

subroutines, Subroutines, Advantages of Subroutines

from other subroutines, Advantages of Subroutines

call_stride subroutine, The Stride Secondary Structure Predictor, The Stride Secondary Structure Predictor

capturing in patterns, Capturing Matched Patterns

carboxyl group, The Organization of Proteins

carriage returns, Getting User Input from the Keyboard, Regular expressions and character classes

matching with metasymbols, Regular expressions and character classes

removing with chomp function, Getting User Input from the Keyboard

case-insensitive matching, Pattern modifiers, Pattern Modifiers

CDS feature key, Parsing the FEATURES Table

centering text, format and write

central dogma of molecular biology, Background

CGI.pm module, creating interactive web pages, Web Programming

chaining, logical operators, Logical Operators and the Range Operator, Using Logical Operators for Control Flow

character classes, Regular expressions and character classes, The Redundancy of the Genetic Code, Using Hashes for the Genetic Code, Regular Expressions, Restriction Enzyme Data, Character classes

genetic code, redundancy of, The Redundancy of the Genetic Code

hash keys and, Using Hashes for the Genetic Code

IUB ambiguity codes, translating to, Restriction Enzyme Data

regular expressions and, Regular expressions and character classes

searching DNA with, Regular Expressions

characters, Representing Sequence Data, Exploding Strings into Arrays, Restriction Enzyme Data

in DNA sequence data, checking source documentation, Exploding Strings into Arrays

letters representing nucleic acids, Representing Sequence Data, Restriction Enzyme Data

chemical bond between amino and carboxyl groups, The Organization of Proteins

children's game with random numbers (example), A Program Using Randomization, A Program Using Randomization

chip-based laboratories for studying gene expression, Microarrays and XML

chmod command, making Perl program executable, Unix or Linux

chomp function, removing newlines with, Getting User Input from the Keyboard

chop function, chomp vs., Getting User Input from the Keyboard

close (system call), Input from Files

close function, Loops

cmp operator, Gene Expression Data Using Sorted Arrays and Binary Search

code, Who This Book Is For, Getting Started with Perl, Pseudocode and Code, Variables, Code Layout, Fixing Bugs in Your Code, Setting breakpoints, Setting breakpoints, Setting breakpoints, Formatting

breakpoints, Setting breakpoints, Setting breakpoints, Setting breakpoints

deleting, Setting breakpoints

debugging, Fixing Bugs in Your Code (see debugging)

examples from this book, downloading, Who This Book Is For

formatting, Code Layout, Formatting

nested function calls, Formatting

Perl, Getting Started with Perl

self-documenting, Variables

subroutines, Pseudocode and Code (see subroutines)

coding DNA, Counting Nucleotides

coding regions, What Are Reading Frames?

codons, Background, Background, Translating Codons to Amino Acids, Using Hashes for the Genetic Code, The Redundancy of the Genetic Code, What Are Reading Frames?

amino acids, representing with, Background

stop, What Are Reading Frames?

translating to amino acids, Translating Codons to Amino Acids, Using Hashes for the Genetic Code, The Redundancy of the Genetic Code

testing for redundant codons, The Redundancy of the Genetic Code

columns, PDB files, PDB File Format

command line, Command-Line Arguments and Arrays, use warnings; and use strict;, How to start and stop the debugger, Input from Files Named on the Command Line

calling Perl interpreter from, use warnings; and use strict;

counting Gs in DNA from, Command-Line Arguments and Arrays

input files, naming on, Input from Files Named on the Command Line

starting Perl debugger from, How to start and stop the debugger

command-line arguments, Command-Line Arguments and Arrays, Command-Line Arguments and Arrays, Command-Line Arguments and Arrays

in @ARGV array variable, Command-Line Arguments and Arrays

commands, Debugger command summary, Command Interpretation

interpretation line, Command Interpretation

Perl debugger, Debugger command summary

comments, Comments, Comments, Comments Revisited, Comments

importance of, Comments

compilers, Getting Started with Perl

compiling Perl source code, Unix and Linux

complementary bases, The Organization of DNA

complex (or imaginary) numbers, Numbers

complex data structures, Complex Data Structures

computation, algorithms for, Algorithms

computer programs, A Low and Long Learning Curve, A Low and Long Learning Curve, Portability, Speed, and Program Maintenance

(see also programming; programs)

defined, A Low and Long Learning Curve

speed of, Portability, Speed, and Program Maintenance

computer science, What Is Bioinformatics?, Biology and Computer Science, Limits to Computation, DNA Computers, Computer Science, General Programming, Algorithms, Software Engineering, General Programming

biology and, What Is Bioinformatics?, Biology and Computer Science, Limits to Computation

limits to solving biology problems, Limits to Computation

programming, Biology and Computer Science

new trends in computing, DNA Computers

resource materials, Computer Science, General Programming, Algorithms, Software Engineering, General Programming

algorithms, Algorithms

general programming, General Programming

software engineering, Software Engineering

computers, A Low and Long Learning Curve

concatenating DNA fragments, Concatenating DNA Fragments, Concatenating DNA Fragments, Concatenating DNA Fragments, Turning Arrays into Scalars with join

join function, using, Turning Arrays into Scalars with join

print statement, using, Concatenating DNA Fragments

concatenating strings, Concatenating DNA Fragments, Making a Sentence, Regular Expressions, String Operators

. (dot) operator, Concatenating DNA Fragments, Making a Sentence

in regular expressions, Regular Expressions

conditional statements, Flow Control, Conditional tests and matching braces, do-until Loops, Conditionals and Logical Operators, The if Statement, Loops

expressions in loops, Loops

testing loops with, do-until Loops

conferences, Conference, Conferences

bioinformatics, Conferences

on Perl, Conference

conservation, measuring sequence similarity by, String Matching and Homology

context, Scalar and List Context

contexts, Scalar and List Context, Scoping

array, Scoping

list and scalar, Scalar and List Context

continue (c) command, Setting breakpoints

control flow, Control Flow, A program with bugs, Control Flow, Using Logical Operators for Control Flow

logical operators, using for, Using Logical Operators for Control Flow

next operator, effect in loops, A program with bugs

in Perl programs, Control Flow

program using randomization, Control Flow

conversion specifiers, The printf Function

copying, Translating DNA into Proteins, Arrays

arrays, Arrays

strings, performance and, Translating DNA into Proteins

counting bases, Operating on Strings, Operating on Strings, Command-Line Arguments and Arrays

on the command line, Command-Line Arguments and Arrays

directly from $DNA string, Operating on Strings, Operating on Strings

counting nucleotides, Counting Nucleotides, Exploding Strings into Arrays, Writing to Files, Writing to Files, Writing to Files

exploding strings into arrays, Exploding Strings into Arrays

global regular expression in while loop test, Writing to Files, Writing to Files

tr function, using, Writing to Files

CPAN (Comprehensive Perl Archive Network), Unix or Linux, Bioperl Tutorial Script, Perl Modules, CPAN: Comprehensive Perl Archive Network

modules, downloading from, Bioperl Tutorial Script

Perl pathnames, problems with, Unix or Linux

current line marker (==>), Stepping through statements with the debugger

cytosine (C), The Organization of DNA, Representing Sequence Data