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Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics
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C

See : cytosine C

c (continue) command

C compiler for Perl source code

call_stride subroutine , 2nd

calling
Perl interpreter from command line

subroutine arguments by reference

subroutine arguments by value

subroutines
from other subroutines

capturing in patterns

carboxyl group

carriage returns
matching with metasymbols

removing with chomp function

case-insensitive matching , 2nd

CDS feature key

centering text

central dogma of molecular biology

CGI.pm module, creating interactive web pages

chaining, logical operators , 2nd

character classes
genetic code, redundancy of

hash keys and

IUB ambiguity codes, translating to

regular expressions and

searching DNA with

characters
in DNA sequence data, checking source documentation

letters representing nucleic acids , 2nd

chemical bond between amino and carboxyl groups

children's game with random numbers (example)

chip-based laboratories for studying gene expression

chmod command, making Perl program executable

chomp function, removing newlines with

chop function, chomp vs.

close (system call)

close function

cmp operator

code
breakpoints
deleting

debugging

examples from this book, downloading

formatting
nested function calls

Perl

self-documenting

subroutines

coding DNA

coding regions

codons
amino acids, representing with

stop

translating to amino acids
testing for redundant codons

columns, PDB files

command line
calling Perl interpreter from

counting Gs in DNA from

input files, naming on

starting Perl debugger from

command-line arguments
in @ARGV array variable

commands
interpretation line

Perl debugger

comments , 2nd , 3rd
importance of

compilers

compiling Perl source code

complementary bases

complex (or imaginary) numbers

complex data structures

computation, algorithms for

computer programs
defined

speed of

computer science
biology and
programming

new trends in computing

resource materials
software engineering

computers

concatenating DNA fragments
join function, using

print statement, using

concatenating strings
. (dot) operator , 2nd

in regular expressions

conditional statements , 2nd
expressions in loops

testing loops with

conferences
bioinformatics

on Perl

conservation, measuring sequence similarity by

context

contexts
array

list and scalar

continue (c) command

control flow
logical operators, using for

next operator, effect in loops

in Perl programs

program using randomization

conversion specifiers

copying
arrays

strings, performance and

counting bases
on the command line

directly from $DNA string

counting nucleotides
exploding strings into arrays

global regular expression in while loop test

tr function, using

CPAN (Comprehensive Perl Archive Network) , 2nd
modules, downloading from

Perl pathnames, problems with

current line marker (==>)

cytosine (C) , 2nd