D

Data Bank of Japan (DBJ), GenBank Files

data bank or data store, databases vs., GenBank

data structures (complex), creating in Perl, Complex Data Structures

data structures for biology, Data Structures and Algorithms for Biology, DBM, Gene Expression Data Using Unsorted Arrays, Gene Expression Data Using Sorted Arrays and Binary Search, Gene Expression Data Using Hashes, Gene Expression Data Using Hashes, Relational Databases

gene expression data, Gene Expression Data Using Unsorted Arrays, Gene Expression Data Using Sorted Arrays and Binary Search, Gene Expression Data Using Hashes

hashes, using for, Gene Expression Data Using Hashes

sorted arrays and binary search, using, Gene Expression Data Using Sorted Arrays and Binary Search

unsorted arrays, using for, Gene Expression Data Using Unsorted Arrays

relational databases, Relational Databases

summary of, Gene Expression Data Using Hashes

data, graphical representation of, Graphics Programming

databases, What Is Bioinformatics?, A Gene Expression Database, Relational Databases, Relational Databases, DBM, GenBank, PDB File Format, PDB File Format

biological data, What Is Bioinformatics?

data banks or data stores vs., GenBank

database management, DBM (see DBM)

gene expression, A Gene Expression Database

PDB files, PDB File Format, PDB File Format

record types, PDB File Format

referenced in, PDB File Format

relational, Relational Databases, Relational Databases

SQL (Structured Query Language), Relational Databases

DBI (Data Base Independence) module, Relational Databases

DBM (database management), DBM, Planning the Program, Indexing GenBank with DBM, Exercises, DBM Essentials, A DBM Database for GenBank, Relational Databases

database for GenBank, A DBM Database for GenBank

different implementations of, DBM Essentials

inadequacy for large projects, Relational Databases

indexing GenBank with, Indexing GenBank with DBM, Exercises

restriction enzymes, storing in, Planning the Program

dbmopen and dbmclose functions, DBM Essentials

DBREF record type, PDB files, PDB File Format, PDB File Format

example, PDB File Format

debuggers, Debugging

debugging, Comments, Fixing Bugs in Your Code, use warnings; and use strict; redux, The Perl Debugger, use warnings; and use strict; redux, How to start and stop the debugger, Debugger command summary, Stepping through statements with the debugger, Stepping through statements with the debugger, Setting breakpoints, Setting breakpoints, Fixing another bug, use warnings; and use strict; redux, A Bug in Your Program?, A Bug in Your Program?

comments, use in, Comments

Mutate DNA program (example), A Bug in Your Program?, A Bug in Your Program?

Perl debugger, using, The Perl Debugger, use warnings; and use strict; redux, How to start and stop the debugger, Debugger command summary, Stepping through statements with the debugger, Stepping through statements with the debugger, Setting breakpoints, Setting breakpoints, Fixing another bug, use warnings; and use strict; redux

breakpoints, Setting breakpoints, Setting breakpoints

command summary, Debugger command summary

my declaration, removing, Fixing another bug

starting and stopping debugger, How to start and stop the debugger

stepping through statements, Stepping through statements with the debugger, Stepping through statements with the debugger

use strict; and use warnings;, use warnings; and use strict; redux

decimal numbers, Randomly Selecting an Element of an Array, Numbers

declaring, Arrays, Exploding Strings into Arrays, Scoping, Scoping, Place a random nucleotide into a random position, A Bug in Your Program?, A Subroutine to Read FASTA Files

arrays, Arrays

my variables, Scoping, Scoping

enforcing with strict pragma, Scoping

variables, Exploding Strings into Arrays, Place a random nucleotide into a random position, A Bug in Your Program?, A Subroutine to Read FASTA Files

beginning of program vs. first use, Place a random nucleotide into a random position, A Bug in Your Program?

in loops, A Subroutine to Read FASTA Files

decrementing variables, Arithmetic Operators

defined and undefined values, true and false

defined function, Using Hashes for the Genetic Code, true and false

DEFINITION field, collecting in GenBank annotations, Using Arrays, Using Arrays

definitions of subroutines, Writing Subroutines

dereferencing, Subroutines: Pass by Reference

designing programs, The Design Phase, Bottom-up Versus Top-down, Object-Oriented Programming

input and output, The Design Phase

object-oriented programming, Object-Oriented Programming

top-down vs. bottom up, Bottom-up Versus Top-down

die function, Output to STDOUT, STDERR, and Files

directives, printf function, The printf Function

directories, in different operating systems, A Low and Long Learning Curve

disease treatment, protein structure and, Protein Data Bank

divisions, GenBank libraries, GenBank Libraries

DNA, The Organization of DNA, The Programming Process, Comments, Representing Sequence Data, Representing Sequence Data, A Program to Store a DNA Sequence, Statements, Concatenating DNA Fragments, Concatenating DNA Fragments, Transcription: DNA to RNA, Transcription: DNA to RNA, Calculating the Reverse Complement in Perl, Calculating the Reverse Complement in Perl, Turning Arrays into Scalars with join, Counting Nucleotides, Counting Nucleotides, Operating on Strings, Operating on Strings, Writing to Files, Writing to Files, Writing to Files, Command-Line Arguments and Arrays, Mutations and Randomization, Exercises, Random Number Generators, A Program Using Randomization, Another Way to Calculate the Random Position, A Program to Simulate DNA Mutation, A Bug in Your Program?, Generating Random DNA, Turning the Design into Code, Analyzing DNA, Some Notes About the Code, The Genetic Code, Exercises, Reading DNA from Files in FASTA Format, A Subroutine to Read FASTA Files, Writing Formatted Sequence Data, Reading Frames, Exercises, What Are Reading Frames?, Background, Separating Sequence and Annotation, Separating annotations from sequence

bases, Representing Sequence Data, Operating on Strings, Operating on Strings

counting in strings, Operating on Strings, Operating on Strings

coding and noncoding, Counting Nucleotides

coding regions, What Are Reading Frames?

concatenating fragments with join function, Turning Arrays into Scalars with join

counting nucleotides in, Counting Nucleotides, Writing to Files, Writing to Files, Writing to Files, Command-Line Arguments and Arrays

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

on the command line, Command-Line Arguments and Arrays

tr function, using, Writing to Files

cutting to insert a gene, Background

mutations, investigating with randomization, Mutations and Randomization, Exercises, Random Number Generators, A Program Using Randomization, Another Way to Calculate the Random Position, A Program to Simulate DNA Mutation, A Bug in Your Program?, Generating Random DNA, Turning the Design into Code, Analyzing DNA, Some Notes About the Code

generating random DNA, Generating Random DNA, Turning the Design into Code

program simulating mutation, A Program to Simulate DNA Mutation, A Bug in Your Program?

program using randomization, A Program Using Randomization, Another Way to Calculate the Random Position

random number generators, Random Number Generators

random sequences, comparing bases for identity, Analyzing DNA, Some Notes About the Code

reading from FASTA files, Reading DNA from Files in FASTA Format, A Subroutine to Read FASTA Files

regulatory elements in, program to count, The Programming Process, Comments

reverse complement of strands, calculating, Calculating the Reverse Complement in Perl, Calculating the Reverse Complement in Perl

separating from GenBank file annotations, Separating Sequence and Annotation, Separating annotations from sequence

sequences, Representing Sequence Data, A Program to Store a DNA Sequence, Statements, Concatenating DNA Fragments, Concatenating DNA Fragments

concatenating, Concatenating DNA Fragments, Concatenating DNA Fragments

program to store, A Program to Store a DNA Sequence

representing, Representing Sequence Data

storing in variables, Statements

transcribing to RNA, Transcription: DNA to RNA, Transcription: DNA to RNA

translating into amino acids and proteins, The Genetic Code, Exercises, Reading Frames, Exercises

reading frames, Reading Frames, Exercises

writing formatted sequence data, Writing Formatted Sequence Data

DNA computers, DNA Computers

do-until loops, do-until Loops, Control Flow, Loops

do-while loops, Loops

documentation, Finding Help, Using the Perl Documentation, Regular Expressions, Obtaining BLAST, Perl, Online Manuals, Basic Operators

BLAST, Obtaining BLAST

Perl, Finding Help, Using the Perl Documentation, Regular Expressions, Perl, Online Manuals, Basic Operators

online manuals, Online Manuals

perlop (for operators), Basic Operators

regular expressions, Regular Expressions

dot (.) operator, Concatenating DNA Fragments (see ., under Symbols)

double helix, The Organization of DNA

downloading, Who This Book Is For, Who This Book Is For, Downloading

(see also resources; web sites)

code examples from this book, Who This Book Is For

Perl, Downloading

droplet, Macperl application, A Program to Store a DNA Sequence

drugs, targeting proteins with, Protein Data Bank