B

backbone residues, primary sequence of, PDB File Format

backslash (\\), Conditional tests and matching braces (see \\, under Symbols)

backups for programs, Saves and Backups

base 16 (hexadecimal) numbers, Numbers

base 8 (octal) numbers, Numbers

bases, The Organization of DNA, The Organization of DNA, The Organization of DNA, Representing Sequence Data, Counting Nucleotides, Counting Nucleotides, Operating on Strings, Operating on Strings, Restriction Enzyme Data, Binding Operators

(see also nucleotides)

complementary nature of, The Organization of DNA

counting, Counting Nucleotides, Counting Nucleotides, Operating on Strings, Operating on Strings

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

pseudocode for, Counting Nucleotides

restriction enzymes, recognition sites, Restriction Enzyme Data

reverse complements, changing to, Binding Operators

Basic Local Alignment Search Tool, Reading DNA from Files in FASTA Format (see BLAST)

beginners in Perl, resources for, Beginners

BeginPerlBioinfo module, downloading, Modules and Libraries of Subroutines

Berkeley DB, DBM Essentials

beta sheets (protein supersecondary structure), Protein Data Bank

beta strands, Protein Data Bank

binary (base 2) numbers, Numbers

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

using with sorted arrays, Gene Expression Data Using Hashes

binary vs. source-code distributions of Perl, Binary Versus Source Code

binding operators, Transcription: DNA to RNA, Pattern matching with =~ and regular expressions, String Matching and Homology, Binding Operators, Binding Operators

!~, Binding Operators

(=~), Transcription: DNA to RNA, Pattern matching with =~ and regular expressions, String Matching and Homology

string matching with, String Matching and Homology

bioinformatics, What Is Bioinformatics?, Modules and Libraries of Subroutines, GenBank, Web Programming, Bioinformatics

BeginPerlBioinfo module, downloading, Modules and Libraries of Subroutines

government-funded web sites, GenBank

Internet as source of data, Web Programming

resources, Bioinformatics

biology, Biology and Computer Science, In Silico, In Silico, Limits to Computation, Data Structures and Algorithms for Biology, DBM, Background, Bioinformatics, Conferences, Molecular Biology

computer science and, Biology and Computer Science, In Silico, In Silico, Limits to Computation, Bioinformatics

bioinformatics resources, Bioinformatics

data mangement, In Silico

limits to solving biology problems, Limits to Computation

programming, Biology and Computer Science

simulating experiments, In Silico

conferences covering bioinformatics, Conferences

data structures and algorithms for, Data Structures and Algorithms for Biology, DBM

molecular, Background, Molecular Biology

books about, Molecular Biology

central dogma, Background

bionet file, restriction enzymes, Restriction Enzyme Data

Bioperl modules, BLAST, Bioperl, Bioperl Tutorial Script, Bioperl, Sample Modules, Sample Modules, Bioperl Tutorial Script, Bioperl Tutorial Script, Bioperl

representative sample of, Sample Modules, Sample Modules

tutorial script, Bioperl Tutorial Script, Bioperl Tutorial Script

web site for, Bioperl

web site for downloading, Bioperl

bitwise operators, Seeding the Random Number Generator, Bitwise Operators, Bitwise Operators

& (bitwise and), Bitwise Operators

| (OR operator), Seeding the Random Number Generator

blank line (user input), testing for, Regular expressions and character classes

BLAST (Basic Local Alignment Search Tool), Reading DNA from Files in FASTA Format, GenBank Libraries, BLAST, Exercises, BLAST, Obtaining BLAST, Obtaining BLAST, String Matching and Homology, BLAST Output Files, BLAST Output Files, Parsing BLAST Output, Parsing BLAST Alignments, Presenting Data, format and write, Bioperl Tutorial Script, Bioperl Tutorial Script

Bioperl, using with, Bioperl Tutorial Script, Bioperl Tutorial Script

documentation, Obtaining BLAST

output files, BLAST Output Files, BLAST Output Files, Parsing BLAST Output, Parsing BLAST Alignments, Presenting Data, format and write

parsing, Parsing BLAST Output, Parsing BLAST Alignments

presenting data, Presenting Data, format and write

public database servers, GenBank Libraries

string matching and homology, String Matching and Homology

versions of, BLAST

WU-BLAST implementation, Obtaining BLAST

blocks, Conditional tests and matching braces, Code Layout, Scoping and Subroutines, Statements and Blocks

code layout, making explicit in, Code Layout

bottom-up program design, Bottom-up Versus Top-down

BPLite.pm (Bioperl module for BLAST), Bioperl Tutorial Script

brackets [], Hashes (see , under Symbols)

breakpoints, Setting breakpoints, Setting breakpoints, Setting breakpoints

deleting, Setting breakpoints

built-in functions, Perl, Online Manuals, Built-in Functions, Built-in Functions

listing with descriptions, Built-in Functions, Built-in Functions

online manual, Online Manuals

by reference, Subroutines: Pass by Reference, Subroutines: Pass by Reference, Parsing BLAST Alignments

passing arguments into subroutines, Subroutines: Pass by Reference, Subroutines: Pass by Reference

subroutines, calling arguments by, Parsing BLAST Alignments

by value, Subroutines: Pass by Value, Parsing BLAST Alignments

copying and passing data, Subroutines: Pass by Value

subroutines, calling arguments by, Parsing BLAST Alignments

byte offsets, When to Use Regular Expressions, Main Program, A DBM Database for GenBank

GenBank records, storing as values, A DBM Database for GenBank

reporting with tell function, Main Program