|
|
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]
P p (print) command
parallelization
See : arguments parameters
parse_blast subroutine , 2nd
parse_blast_alignment subroutine
parse_blast_alignment_HSP subroutine
parseATOM subroutine
parsePDBrecordtypes subroutine
parsingBLAST output files alignments
GenBank file annotations using regular expressions
PDB files SEQRES record
REBASE files
stride program output
passing by reference , 2nd
dereferencing
passing by value
pathnames modules
Perl programs
pattern matching
pattern modifiers
patterns (and regular expressions) , 2nd
alternation in
ATOM record type, extracting from PDB file
binding operators
character classes and
choices, separating with vertical bar (|)
closure in
concatenation in
example of regular expressions
extract_sequence_from_data subroutine
extracting annotations and alignments (BLAST files)
GenBank annotations, parsing
GenBank records, operating on
genetic code, redundancy in
global regular expression in while loop test
hash keys and
IUB ambiguity codes, translating to
matching regular expression, using as conditional test
metacharacters , 2nd
metasymbols
minimal matching
modifiers /s
PDB file record types, matching
restriction enzymes, representing in
string matching
substitution operator
translating restriction enzymes into
See : Protein Data Bank PDB
Pennsylvania State University, BLAST programs
peptide bond, amino acids
peptide or protein sequence data (.pep file extension)
peptides primary structure of
percent identity, measuring similarity of sequences , 2nd
See : %, under Symbols percent sign
performance copying strings and
exploded strings and
PDB files and
See : . (dot period , under Symbols)
Perl , 2nd
arithmetic operations
arrays
assignment
bioinformatics modules
Bioperl modules
built-in functions
command interpretation
comments , 2nd
conditional statements logical operations and
controlling other programs from
CPAN (Comprehensive Perl Archive Network) , 2nd
DBM (database management)
documentation
ease of programming
hashes
help, finding
home page
input/output
installing
language, applications vs.
latest stable release, web site for
loops , 2nd
modules object-oriented programming and
operators
portability, speed and program maintenance
rapid prototyping
regular expressions
reserved words
resource materials
reverse complement, calculating
running programs
scalar and list context
scalar values
statements blocks and
style guide
subroutines , 2nd
text data, ease of manipulating
text editors for writing programs
variables scalar
versions of
perldoc perlstyle
perlop documentation
picture fields
picture line, specifying test layout
piping debugger output through pager
PIR (Protein Identification Resource)
plain text, saving data as
polymers DNA
protein
pop function arrays, using with
portability
pos function
positions in arrays
precedence arithmetic operations
logical operators , 2nd
operator
presenting data, BLAST output files
primary structure, proteins , 2nd
print function , 2nd
arrays, handling
print statements concatenating DNA fragments with
newlines
print_sequence subroutine
printf function
printing arrays with spaces between elements
to a file
number stored in scalar variable
p (print) command
to STDOUT
procedural knowledge
procedural programming
programming algorithms
for biologists
debugging
environment of programs
error messages, interpreting
general, resource material
graphics
maintenance of programs
object-oriented
Perl summary of language
process of pseudocode and code
for relational databases
saving and backing up code
strategies for
web
programming languages
programs command line, running from
debugging
exiting
external, automating with Perl
main section or main body of
Perl text editors for
rapid prototyping with Perl
Protein Data Bank (PDB) , 2nd
controlling external programs from Perl
files SEQRES record, parsing
files and folders
parsing files finding atomic coordinates
three-dimensional structures, macromolecules
web site
proteins coding regions in DNA
DNA coding for
DNA, translating into FASTA file, reading and formatting output
homology of
motifs, finding PROSITE web site
organization of
Protein Identification Resource (PIR)
RNA, translation into
sequences representing
structure of
pseudo-random numbers
pseudocode commenting out
for counting nucleotides
DNA regulatory elements, counting
getanswer (example)
public database servers
push function adding element at end of array
arrays, using with
|
