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Beginning Perl for Bioinformatics

Beginning Perl for Bioinformatics
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R
rand function , 2nd

random number generators
seeding

randomelement subroutine (example)

randomization , 2nd
comparing bases in random DNA sequences

generating random DNA
subroutines for

program simulating mutation
random position in string, selecting

program using
selecting array elements randomly

random number generators

randomnucleotide subroutine (example) , 2nd
improving design

range operator (..), using with logical operators

rapid prototyping

rational numbers

ratios

raw score (S), BLAST matching

reading
bionet file for restriction sites

DNA from FASTA files

FASTA format files
subroutine for

files

PDB files

protein sequence data from a file, using while loop

restriction enzyme data

reading frames
ORFs (open reading frames)

translating DNA in

translating DNA in all, main program

REBASE (Restriction Enzyme Database)
data file, subroutine for parsing

recognition sites
codes for

IUB nucleic acid codes, translating to regular expressions

records, GenBank files
fields

separating annotation from sequence
using scalars

records, PDB files
names

types
parsePDBrecordtypes subroutine

Red Hat Linux systems, rpm files

redundancy in genetic code , 2nd

reference_sub subroutine

references
calling by

complex data structures and

to databases in PDB files

DBREF record type, PDB files

dereferencing

passing by

See : patterns regular expressions

regulatory elements in DNA, program that counts
design phase

relational database management systems (RDMS)

relational databases
DBI (Perl module)

programming for

removing
carriage returns, linefeeds, and newlines

my variables (in debugging)

newlines and other nonsequence data

newlines from filenames

whitespace , 2nd

repeating strings (x operator)

See : graphical user interfaces representation of data

reserved words

residues in macromolecule chains
amino acid or nucleic acid sequence of

resources
bioinformatics

computer science

molecular biology

Perl

Restriction Enzyme Database (REBASE)
data file, subroutine for parsing

restriction enzymes
data, bionet file format

reading data from file

storing data

user requests for names

web site information on

restriction maps , 2nd , 3rd
computing

recognition sites (IUB nucleic acid codes), translating to regular expressions

reporting to user

restriction sites
reading bionet file for

return values, subroutine

reverse complements
calculating in Perl

changing bases into

DNA transcription to RNA

restriction enzyme EcoRI

subroutine for computing (revcom)

reversing arrays

right justification of text

right shift (>>) operator

RNA (ribonucleic acid)
DNA, transcribing to

transcribing DNA to

rpm files, Red Hat Linux

running Perl programs
on Macintosh

on Windows

rvalue and lvalue