Practical Exercises Bioinformatics I: Sequence Analysis and Phylogenetics
| Course no.: | 365.027 (4KV) |
| Lecturer: | Karin Schwarzbauer |
| Mode: | 2 hours, weekly |
| Times/locations: | Wed, 10:15-11:45, KG 712 |
| Start: | Wed, Oct 6, 2010 |
| Registration: | KUSSS |
Exercises in Bioinformatics
| Course no.: | 365.052 (2UE) |
| Lecturer: | Günter Klambauer |
| Mode: | 2 hours, weekly |
| Times/locations: | Wed, 10:15-11:45, T 212 |
| Start: | Wed, Oct 6, 2010 |
| Registration: | KUSSS |
Goals
To practize the concepts and methods presented in the lecture Bioinformatics I: Sequence Analysis and Phylogenetics.Assignments
You will receive weekly assignments with examples that you must solve. In the next course after the submission deadline, the submissions are discussed and students are asked to present their results. Points are deducted in case that a student has insufficient knowledge of his/her own homework. For passing the course successfully, 60% of the points need to be achieved.
Before submitting any homework, read the instructions for submitting homework carefully!
Supplementary Material (Data, Programs)
- igenome.seq (620Byte; last update: 2008-10-09)
- BLOSUM62.txt (3KB; BLOSUM62 matrix in BLAST format)
- ReadScoringMatrix.pl (3KB; Perl sub-routine for reading a scoring matrix from a file)
Slides of Perl Tutorial
- Perl-Tutorial.pdf (319KB; last update: 2008-10-15)
Perl Examples
Download all examples: Perl-Examples.zip (3KB; last update: 2007-08-07)
The following programs are contained in this archive:
- empty.pl: empty template (she'bang line and use strict;)
- helloworld.pl: "the mother of programs"
- testquotes.pl: demonstrates the difference between single and double quotes
- divider.pl: simple example for using subroutines
- simple_election.pl: simple example using hashes
- election.pl: more sophisticated variant of simple_election.pl
- lobalglobal.pl: examples demonstrating the difference between local and global variables
- test_regexp.pl: examples of regular expressions
- testrelist.pl: examples for extracting matches from regular expressions
- testdoublehash.pl: examples for hashes of hashes
Perl Software and Documentation
- ActivePerl
- Introduction and overview of Perl (PDF, 63KB)
- Perl functions reference
- Perl regular expressions tutorial
- The Perl Directory