A

A, The Organization of DNA (see adenine)

accession numbers (GenBank records), storing as keys, A DBM Database for GenBank

active site of a protein, Protein Data Bank

ActivePerl from ActiveState, Windows

adenine (A), The Organization of DNA, Representing Sequence Data

algorithms, Algorithms, Data Structures and Algorithms for Biology, A Gene Expression Database, Gene Expression Data Using Sorted Arrays and Binary Search, Gene Expression Data Using Hashes, String Matching and Homology, String Matching and Homology, Algorithms and Sequence Alignment, Algorithms and Sequence Alignment, Modeling Networks, Algorithms

binary search, Gene Expression Data Using Sorted Arrays and Binary Search, Gene Expression Data Using Hashes

using with sorted arrays, Gene Expression Data Using Hashes

data structures and, Data Structures and Algorithms for Biology, A Gene Expression Database

gene expression database, A Gene Expression Database

graph, modelling biological networks, Modeling Networks

resource materials, Algorithms

sequence alignment and, Algorithms and Sequence Alignment

string matching, String Matching and Homology, String Matching and Homology, Algorithms and Sequence Alignment

(see also BLAST)

alignment (sequence), algorithms and, Algorithms and Sequence Alignment

alignment of text, format and write

alignments, BLAST, Extracting Annotation and Alignments, Extracting Annotation and Alignments, Parsing BLAST Alignments, Parsing BLAST Alignments

extracting, Extracting Annotation and Alignments, Extracting Annotation and Alignments

parsing, Parsing BLAST Alignments, Parsing BLAST Alignments

alpha helices, beta-strands, and turns, Protein Data Bank

alpha-alpha units (protein supersecondary structure), Protein Data Bank

alphabetical sorting, array of strings, Gene Expression Data Using Sorted Arrays and Binary Search

alphabets (nucleic acid and amino acid codes), Representing Sequence Data

alternation, Regular Expressions, Alternation with |

amino acids, The Organization of Proteins, Representing Sequence Data, Representing Sequence Data, The Genetic Code, Using Hashes for the Genetic Code, Background, What Are Reading Frames?

codes for (standard IUB/IUPAC), Representing Sequence Data

lacking stop codons, What Are Reading Frames?

translating DNA into, The Genetic Code, Using Hashes for the Genetic Code, Background

representing with codons, Background

amino group, The Organization of Proteins

and operator, Logical Operators and the Range Operator, Logical Operators and the Range Operator, Bitwise Operators, Logical Operators, Using Logical Operators for Control Flow

bitwise and (&) operator, Bitwise Operators

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

control flow, using for, Using Logical Operators for Control Flow

angle brackets (), Exploding Strings into Arrays (see , under Symbols)

angle operator, Reading Proteins in Files, Getting User Input from the Keyboard, Finding Atomic Coordinates, Input from Files Named on the Command Line

annotations, BLAST files, Extracting Annotation and Alignments, Extracting Annotation and Alignments, Parsing BLAST Alignments

extracting, Extracting Annotation and Alignments, Extracting Annotation and Alignments

HSPs, Parsing BLAST Alignments

annotations, GenBank files, GenBank, GenBank Files, Separating Sequence and Annotation, Separating annotations from sequence, Parsing Annotations, When to Use Regular Expressions, Using Arrays, Using Arrays, When to Use Regular Expressions, When to Use Regular Expressions, Parsing Annotations at the Top Level, Parsing Annotations at the Top Level, Parsing the FEATURES Table, Parsing

information in, GenBank Files

parsing, Parsing Annotations, When to Use Regular Expressions, Using Arrays, Using Arrays, When to Use Regular Expressions, When to Use Regular Expressions, Parsing Annotations at the Top Level, Parsing Annotations at the Top Level, Parsing the FEATURES Table, Parsing

at top-level, Parsing Annotations at the Top Level, Parsing Annotations at the Top Level

FEATURES table, Parsing the FEATURES Table, Parsing

using arrays, Using Arrays, Using Arrays

using regular expressions, When to Use Regular Expressions, When to Use Regular Expressions

separating from DNA sequences, Separating Sequence and Annotation, Separating annotations from sequence

applications (Perl), programming language vs., Getting Started with Perl

Applied Biosystems (ABI) sequencer output, Reading DNA from Files in FASTA Format

approximation, Algorithms and Sequence Alignment

argument line, format and write

arguments, Writing Subroutines, Writing Subroutines, Arguments, Scoping, Command-Line Arguments and Arrays, Command-Line Arguments and Arrays, Command-Line Arguments and Arrays, Subroutines: Pass by Reference, Subroutines: Pass by Reference, Subroutines: Pass by Reference, Subroutines and Modules

@_ arrays, passing into subroutines with, Subroutines: Pass by Reference

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

@ARGV array variables, Command-Line Arguments and Arrays

passing by reference, Subroutines: Pass by Reference, Subroutines: Pass by Reference

dereferencing, Subroutines: Pass by Reference

scoping and, Scoping

separating with commas, Writing Subroutines

arithmetic operators, Precedence of Operations and Parentheses, Arithmetic Operators

order of evaluation, Precedence of Operations and Parentheses

array context, putting variables into, Scoping

arrays, Arrays, Scalar and List Context, Arrays, Arrays, Arrays, Scalar and List Context, Scalar and List Context, Turning Arrays into Scalars with join, Counting Nucleotides, Exploding Strings into Arrays, Operating on Strings, Arguments, Command-Line Arguments and Arrays, Command-Line Arguments and Arrays, Command-Line Arguments and Arrays, Subroutines: Pass by Reference, Subroutines: Pass by Reference, Stepping through statements with the debugger, A Program Using Randomization, A Program Using Randomization, Randomly Selecting an Element of an Array, Formatting, Formatting, Another Way to Calculate the Random Position, Improving the Design, Hashes, Hashes, 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, Using Arrays, Using Arrays, Using Arrays, Extracting Primary Sequence, Arrays, Input from Files Named on the Command Line, Subroutines and Modules

@ARGV, Input from Files Named on the Command Line

@_ arrays, Arguments, Subroutines: Pass by Reference

associative, Hashes (see hashes)

converting to scalar variables, Turning Arrays into Scalars with join

elements, Operating on Strings, Command-Line Arguments and Arrays

extracting from, Command-Line Arguments and Arrays

numbering positions of, Operating on Strings

exploding strings into, Counting Nucleotides, Exploding Strings into Arrays

GenBank annotations, parsing with, Using Arrays, Using Arrays

GenBank records, using with, Using Arrays

of hash key/value pairs, Hashes

initializing and accessing individual elements, Arrays

inserting element at arbitrary position in, Arrays

in list context, Scalar and List Context

multiline strings, converting to, Extracting Primary Sequence

passing by reference into or out of subroutines, Subroutines: Pass by Reference

printing, Stepping through statements with the debugger

randomly selecting elements from, A Program Using Randomization, A Program Using Randomization, Randomly Selecting an Element of an Array, Formatting, Another Way to Calculate the Random Position, Improving the Design

alternate method, Another Way to Calculate the Random Position

formatting nested function calls, Formatting

subroutines for, Improving the Design

reversing, Arrays

in scalar context, Scalar and List Context

size, determining (scalar function), Formatting

sorted, for gene expression data, Gene Expression Data Using Sorted Arrays and Binary Search

as subroutine arguments, Subroutines and Modules

unsorted, for gene expression data, Gene Expression Data Using Unsorted Arrays

using with push and pop functions, Gene Expression Data Using Hashes

using with push and shift functions, Gene Expression Data Using Hashes

ASCII, Representing Sequence Data, GenBank, Overview of PDB

flat files, GenBank, Overview of PDB

GenBank, GenBank

PDB (Protein Data Bank), Overview of PDB

assignment, Statements, Assignment, Concatenating DNA Fragments, Transcription: DNA to RNA, Scalar and List Context, Scalar and List Context, Assignment, Scalar and List Context

= operator, use in statements, Assignment

array to scalar variable, Scalar and List Context

arrays to lists, Scalar and List Context

in concatenation of DNA fragments, Concatenating DNA Fragments

in DNA to RNA transcription, Transcription: DNA to RNA

scalar and list context, Scalar and List Context

assignment operators, Assignment, Assignment

associative arrays, Hashes (see hashes)

atomic coordinates, finding in PDB files, Finding Atomic Coordinates, Finding Atomic Coordinates, Finding Atomic Coordinates, Finding Atomic Coordinates

ATOM record type, Finding Atomic Coordinates, Finding Atomic Coordinates

parsing from input file, Finding Atomic Coordinates

attributes, file, Operating on Strings

autoincrement and autodecrement operators, Arithmetic Operators

automating programs, Controlling Other Programs, The Stride Secondary Structure Predictor, The Stride Secondary Structure Predictor

secondary structure predictor, The Stride Secondary Structure Predictor, The Stride Secondary Structure Predictor