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Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics
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B
backbone residues, primary sequence of

    See : \\\\, under Symbols backslash (\\\\)

backups for programs

base 16 (hexadecimal) numbers

base 8 (octal) numbers

bases , 2nd , 3rd
complementary nature of

counting
pseudocode for

restriction enzymes, recognition sites

reverse complements, changing to

    See : BLAST Basic Local Alignment Search Tool

beginners in Perl, resources for

BeginPerlBioinfo module, downloading

Berkeley DB

beta sheets (protein supersecondary structure)

beta strands

binary (base 2) numbers

binary search algorithm
using with sorted arrays

binary vs. source-code distributions of Perl

binding operators
!~

(=~)
string matching with

bioinformatics
BeginPerlBioinfo module, downloading

government-funded web sites

Internet as source of data

resources

biology
computer science and
simulating experiments

conferences covering bioinformatics

data structures and algorithms for

molecular
central dogma

bionet file, restriction enzymes

Bioperl modules , 2nd
representative sample of

tutorial script

web site for

web site for downloading

bitwise operators
& (bitwise and)

| (OR operator)

blank line (user input), testing for

BLAST (Basic Local Alignment Search Tool) , 2nd
Bioperl, using with

documentation

output files
presenting data

public database servers

string matching and homology

versions of

WU-BLAST implementation

blocks , 2nd , 3rd
code layout, making explicit in

bottom-up program design

BPLite.pm (Bioperl module for BLAST)

    See : , under Symbols brackets []

breakpoints
deleting

built-in functions, Perl
listing with descriptions

online manual

by reference
passing arguments into subroutines

subroutines, calling arguments by

by value
copying and passing data

subroutines, calling arguments by

byte offsets
GenBank records, storing as values

reporting with tell function