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Beginning Perl for Bioinformatics | |
Beginning Perl for Bioinformatics
[Symbol][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][X]
S s (single step) command
s/// (substitution) operator , 2nd
regular expressions, use with
saving programs
scalar context , 2nd
arrays in
scalar function determining size of arrays
scalar values assigning to arrays
assigning to scalar variables
numbers
strings
scalar variables $ (dollar sign), beginning with
arrays, converting to
assigning scalar values to
assignment operator, setting value with
datatypes held in
GenBank records, reading as
printing out values
references, storing in
storing numbers in
user input, saving as
scientific (exponential) notation
scoping , 2nd
strict
variables within while loop
scores and statistics on matches, BLAST program
scripts (Perl)
search_annotation subroutine
secondary structures, proteins , 2nd
predictor program (stride)
seeding random number generators , 2nd
seek function
self-documenting code
sentences, randomly combining parts of
SEQADV record type, PDB files example
SEQRES record type, PDB files parsing
sequences alignment methods
DNA program to store
protein reading from file with while loop
removing nonsequence data from
representing
similarity, statistical methods to calculate
servers BLAST, web sites for
public database
shift function , 2nd
taking element from beginning of array
similarity as indication of homology
simple data (Applied Biosystems (ABI) sequencer output)
simulating DNA mutation , 2nd
program (mutate DNA)
program, designing random position in string, selecting
simulating experiments with computers
single line (/s pattern modifier)
single step (s) command
size of arrays
Smith-Waterman algorithm for sequence alignment
software (bioinformatics), distribution sites
software engineering
sort function
sorted arrays in gene expression data
using with binary search algorithm
sorting alphabetical, array of strings
array of numbers
hash keys and values
source code comments
open source
Perl distributions Unix or Linux, downloading on
source feature key
speed, Perl programs
splice function
split function hash values, using on
multiline strings, converting to arrays
strings, extracting data from
sprintf function
SQL (Structured Query Language)
srand function
standard residues, modifications to
statements , 2nd
block
flow control
See : lexical scoping static scoping
statistical methods to calculate sequence similarity
STDERR filehandle
STDIN filehandle
STDOUT filehandle printing to
stop codons
stop signals
strands of DNA, calculating reverse complement
strict pragma , 2nd
, 3rd
variables, finding errors in
stride program, secondary structure predictor parsing output
string interpolation
strings , 2nd
arrays of, sorting alphabetically
binding operators
capturing matched patterns in
comparing alphabetically in Perl
concatenating in regular expressions
copying, performance and
empty
exploding into arrays
finding motifs in
formatting (sprintf function)
length of
long, DMB handling of
matching algorithms for
multiline using regular expressions on
newlines, removing from ends
numbering positions in translate_frame subroutine
operating on tr (transliteration) function
operators
quotes, use in
selecting random position in
specific positions, examining
split function, extracting data with
substituting characters in (tr/// operator)
whitespace, removing from end
structure of DNA
primary, of peptide or nucleotide sequence
of proteins
structured design
style guide, Perl
subroutines , 2nd
, 3rd
, 4th
advantages of
appending ACGT to DNA (example)
arguments
call by reference
call_stride
calling other subroutines
command-line arguments and arrays
definitions placement of
extract_HSP_information
extract_sequence_from_fasta_data
extracting annotation from sequence, GenBank files
extractSEQRES
GenBank library testing
get_file_data , 2nd
getanswer (example)
IUB ambiguity codes, translating to regular expressions
iub3to1 (converting PDB character codes)
match_positions (example)
modules and libraries of
mutate (example) debugging
mutate_better (example)
object-oriented programming, interfacing with
parse_blast
parse_blast_alignment
parse_blast_alignment_HSP
parse_stride
parseATOM
parsePDBrecordtypes
parsing REBASE data file
parsing REBASE files
passing data to by value
random DNA set, generating
random number generator
randomelement (example)
randomnucleotide (example) improving design
randomposition (example)
reading FASTA files
redundant codons, testing for
return values
returning sequence data from FASTA format
reverse complement, computing
scoping and
search_annotation
translating DNA codons to amino acids using hash lookup
translating DNA frames, computing indices
translating DNA to peptide
variables in
writing
writing formatted sequence data
subscripts, array elements integer values for
substitution (s///) operator , 2nd
, 3rd
substr function , 2nd
, 3rd
supersecondary structures
syntax errors
system calls checking success or failure of
open and close
open, using with unless statement
system function
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