Safari | Beginning Perl for Bioinformatics










Beginning Perl for Bioinformatics
   Copyright
   Table of Contents
  Preface
  1. Biology and Computer Science
  2. Getting Started with Perl
  3. The Art of Programming
  4. Sequences and Strings
  5. Motifs and Loops
  6. Subroutines and Bugs
  7. Mutations and Randomization
  8. The Genetic Code
  9. Restriction Maps and Regular Expressions
  10. GenBank
  11. Protein Data Bank
  12. BLAST
  13. Further Topics
  A. Resources
  B. Perl Summary
   Colophon
  Index










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] ! (bang) ! (logical negation) operator , 2nd

 != (not equal to) operator
 !~ (binding) operator
 #! (shebang) notation

" (quotes, double) within double-quoted strings
 empty strings, representing with
 string interpolation
 in strings , 2nd


 "exclusive-OR" operator (xor) , 2nd

 "point-and-click" interaction with data
# (sharp) #! (shebang notation), command interpretation line
 in Perl comments

$ (dollar sign) for scalar variable names , 2nd

 $$, returning Perl program ID number
 $& variables , 2nd

 $' variables
 $/ (input record separator)
 $_ variables , 2nd
 , 3rd

 $` variables
 before embedded newlines
 metacharacter
 metacharacter in regular expressions

 $PATH or $path variable
% (percent sign) in directives
 for hash names , 2nd


& (ampersand) && (logical and) operator , 2nd

 (bitwise and) operator
 subroutine names, starting with

' (quotes, single) empty strings, representing with
 in strings , 2nd


() (parentheses) for capturing in patterns
 enclosing subroutine arguments
 grouping in regular expressions , 2nd

 in regular expressions
 metacharacter in regular expressions
 order of operations, specifying with
 variables from @_ array, enclosing with

(angle brackets)> (right angle bracket) right justification

< (left angle bracket) less than operator

 line input (angle) operator , 2nd
 , 3rd
 , 4th


* (asterisk) *? quantifier
 character wildcard
 quantifier
 in regular expressions

+ (plus sign) ++ (autoincrement) operator , 2nd

 += (add assignment) operator
 quantifier

, (comma) separating items in lists
 separating subroutine arguments

 -- (minus sign), autodecrement operator
 -d (debug) command-line switch
 -e (exists) file test
 -w command-line switch, turning on warnings
. (dot) .. (range) operator
 character wildcard , 2nd

 metacharacter in regular expressions
 string concatenation operator , 2nd


/ (forward slash)// (double slash) end-of-record separator

 in pattern modifiers
 s/// (substitution) operator

 /g (global) pattern modifier , 2nd

 /i (case-insensitive) matching , 2nd

 /m pattern modifier , 2nd
 program to extract annotation from sequence

 /s pattern modifier program to extract annotation from sequence

 ; (semicolon), ending Perl statements , 2nd

= (equal sign) == (equal to) operator
 ==> current line marker
 =~ (pattern binding) operator , 2nd
 , 3rd

 assignment operator , 2nd


 ? (question mark), in quantifiers
@ (at sign) @_ arrays , 2nd

 @ARGV array variables
 beginning array variables with
 for array names

 @ARGV arrays
[] (brackets) array element lookups
 enclosing character class in

\\\\ (backslash) escaping metacharacters
 escaping quotes within quoted strings
 metasymbols, use in
 references, use in

 \\\\n or \\\\n\\\\n (newlines)
^ (caret) beginning of string, anchoring to
 bitwise xor operator
 end of line assertion (in matching)
 for filled text in formats
 metacharacter in regular expressions , 2nd
 , 3rd

 restriction enzyme cut site (REBASE)

 ` (backticks), command input operator
{} (curly braces) hash lookups, use in
 quantifier
 for statement blocks
 in string interpolation

| (vertical bar) (bitwise OR) operator , 2nd

 || (logical or) operator , 2nd

 alternation
 for centering
 debugger commands
 regular expressions, use in

 ~~ (tildes), for multiline data in fields
 3' (three prime) end, nucleotides
 3D protein structure , 2nd
 , 3rd

 5' (five prime) end, nucleotides
A    See : adenine A
 accession numbers (GenBank records), storing as keys
 active site of a protein
 ActivePerl from ActiveState
 adenine (A) , 2nd

 algorithmsbinary search using with sorted arrays

data structures and gene expression database

 graph, modelling biological networks
 resource materials
 sequence alignment and
 string matching , 2nd


 alignment (sequence), algorithms and
 alignment of text
alignments, BLAST extracting
 parsing

 alpha helices, beta-strands, and turns
 alpha-alpha units (protein supersecondary structure)
 alphabetical sorting, array of strings
 alphabets (nucleic acid and amino acid codes)
 alternation , 2nd

 amino acids , 2nd
 codes for (standard IUB/IUPAC)
 lacking stop codons
translating DNA into representing with codons


 amino group
and operator bitwise and (&) operator
logical and control flow, using for


    See : , under Symbols angle brackets ()
 angle operator , 2nd
 , 3rd
 , 4th

annotations, BLAST files extracting
 HSPs

 annotations, GenBank files information in
parsing using regular expressions

 separating from DNA sequences

 applications (Perl), programming language vs.
 Applied Biosystems (ABI) sequencer output
 approximation
 argument line
 arguments , 2nd
 , 3rd
 @_ arrays, passing into subroutines with
command-line @ARGV array variables

passing by reference dereferencing

 scoping and
 separating with commas

 arithmetic operators order of evaluation

 array context, putting variables into
 arrays , 2nd
 , 3rd
 @_ arrays , 2nd

 @ARGV
 associative
 converting to scalar variables
elements numbering positions of

 exploding strings into
 GenBank annotations, parsing with
 GenBank records, using with
 of hash key/value pairs
 initializing and accessing individual elements
 inserting element at arbitrary position in
 in list context
 multiline strings, converting to
 passing by reference into or out of subroutines
 printing
randomly selecting elements from subroutines for

 reversing
 in scalar context
 size, determining (scalar function)
 sorted, for gene expression data
 as subroutine arguments
 unsorted, for gene expression data
 using with push and pop functions
 using with push and shift functions

 ASCIIflat files PDB (Protein Data Bank)


 assignment , 2nd
 = operator, use in statements
 array to scalar variable
 arrays to lists
 in concatenation of DNA fragments
 in DNA to RNA transcription
 scalar and list context

 assignment operators , 2nd

    See : hashes associative arrays
 atomic coordinates, finding in PDB filesATOM record type parsing from input file


 attributes, file
 autoincrement and autodecrement operators
 automating programs secondary structure predictor







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