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Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics
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M
Macintosh
filesystem

finding Perl (already installed)

installing Perl on

Perl versions for

running Perl programs

text editors

MacOS X
already installed Perl, finding

Perl version, displaying

running Perl programs

specifying input files on command line

Macperl application, saving files as droplets

macromolecules
3D structures of

residues, amino acid or nucleic acid sequence of

mailing lists for Perl beginners

main program or main body of a program

maintaining programs

make_random_DNA_set subroutine (example)

manuals (online), for Perl

match_positions subroutine (example)

See : patterns matching patterns

maximal (greedy) matching

metacharacters , 2nd , 3rd
parentheses, in regular expressions

metasymbols , 2nd

methods, object-oriented programming

microarray technology , 2nd

minimal matching

modelling biological networks

modes (file permission), DBM files

See : patterns, modifiers modifiers, pattern matching

MODRES record type, PDB files

modules
Bioperl
web site for downloading

CPAN (Comprehensive Perl Archive Network) , 2nd

for creating web pages

last line in

object-oriented programming and

of subroutines
pathnames

molecular biology
books about

central dogma of

motifs , 2nd
finding in strings

newlines, eliminating with join

protein (PROSITE web site)

searching for with character classes

multiline information sets, GenBank vs. PDB

multiline strings
/m pattern modifier and , 2nd

converting to arrays

mutate subroutine (example)
debugging

mutate_better subroutine (example)

mutations, investigating with randomization
generating random DNA
subroutines for

program simulating mutation
random position in string, selecting

program using randomization
selecting array position, randomly

random number generators

my variables , 2nd , 3rd
pitfalls of not using

removing to debug code