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]F false or true value, evaluating with conditionals , 2nd

 FAQs, Perl , 2nd
 newsgroup information

 FASTA format, DNA sequences reading and extracting sequence data, main program
 reading and formatting file output
reading files subroutine for


 FEATURES table (GenBank annotations)feature keys parsing


 fields, GenBank records PDB record types vs.

 file permission modes, DBM files
 file test operators , 2nd
 -e (exists)

 File\:\:Find module
 filehandles , 2nd
 , 3rd
 output

 filenames, removing newlines from
filesASCII flat files PDB

 attributes, testing for
BLAST output presenting data

 directing output to
 FASTA format, reading DNA from
input from named on command line

 naming
opening with system calls

PDB parsing

 protein sequence data, reading from
 writing to

 filesystems
 flags, use of
 floating-point numbers , 2nd

 flow control bad code format and
 conditional statements
 loops

folders Macintosh or Windows
 naming
 PDB

 folding of proteins
 for loops , 2nd
 here document in
 initialization and increment of counter
 program using randomization

 foreach loops , 2nd
 , 3rd
 , 4th
 $_ variables in
 variable declaration in

 fork function
 format function , 2nd

 formats, DNA files
 formatted sequence data, writing
formattingcode function calls in nested braces

output printf function
 , 2nd



 formfeeds, matching with metasymbols
 fractions , 2nd

 frequently asked question lists (FAQs), Perl
functions built-in
 nested calls, formatting in code
 Perl, online manual







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