Biochem 508, Spring 2009

Perl Programming Supplement

Friday 2:00 - 3:00
ITC/ACHS, Biochemistry Library

Suggested Text:
Beginning Perl, 2nd ed., Lee, James, Apress (2004) ISBN 159059391X Amazon

Additional Texts:
Programming Perl 3rd Ed. Wall, Christiansen, Orwant (2000) O'Reilly ISBN 0-596000-27-8 Amazon

Other Texts:
Learning Perl 5th Ed. Schwartz, Phoenix, and Foy (2008) O'Reilly ISBN 0596520107 Amazon

Beginning Perl for Bioinformatics Tisdall (2001) O'Reilly ISBN 0-596-00080-4 FatBrain

Perl Tutorials

http://www.perl.com/pub/a/2008/04/23/a-beginners-introduction-to-perl-510.html - Excellent focussed introduction.

learn.perl.org - A WWW site devoted to learning Perl.

Jan28 Introduction to Editors, Perl, perldoc [pdf]
Exercises:
  1. Unix -- login/transfer a sequence file from your computer to xi00.achs
  2. Emacs -- edit the file -- make a duplication in the middle of the sequence
  3. Unix -- download the file back to your computer
  4. Unix -- Run the FASTA program with your sequence. Save the output to
  5. Unix -- Run the lalign program to find the duplication
  6. Perl -- Print a random number
Feb4 Scalars, Arrays, Hashes, Control Structures [pdf]
Exercise: Print a random DNA or protein sequence
11Input/Output, Subroutines,Regular Expressions, string manipulations
Exercise: Extract score information from a FASTA search
18Modules - LWP get, CGI, Object oriented modules, BioPerl, LWP::UserAgent [pdf]
Exercise: Download a sequence from NCBI

wrp@virginia.edu

Last modified: Monday, 26-Jan-2009 10:45:15 EST