Module Title

Module Title

Module Code

Credits 

Courses and year of study for which module is designed

Semester(s) in which module is taught

Module Coordinator

Date submitted to LTA Committee

Module Overview:

General Aims:

Learning Outcomes:

• 
  foundation programming skills in Perl and to perform core bioinformatic tasks
  
• 
  understand the scope for further learning and more advanced applications
  
• 
  appreciate that computer-based tools are fundamental to modern biology and medicine
  

Module Assessment:

1. 
   oneliners; awk; bash vs c-shell; creating scripts; warnings
   
2. 
   printing; aliases; standard input/output; opening/closing files
   
3. 
   my variables; scalars; strings; arrays; die; if-else; and/or;
   
4. 
   undefined variables; while; for; unless; until
   
5. 
   pattern matching; motif searching; printf statements
   
6. 
   translating DNA/protein sequences; sequence processing
   
7. 
   homology searching using scripts to implement tools, accessing websites
   
8. 
   debugging; sub-routines; script structure
   
9. 
   example application: testing rates of molecular evolution in DNA (eg PAML)
   
10. 
    hashes – format, usage and applications
    
11. 
    example application: processing high-throughput DNA sequence data
    
12. 
    modular programming; online resources; other languages
    

1. 
   write Perl/awk/shell commands to denote columns in a fasta text file
   
2. 
   read in, sort based on user preference, and print to file a set of genes
   
3. 
   denote the amino acid length and present of stop codons in a DNA sequence
   
4. 
   do pairwise alignments for all possible sequences in a file
   
5. 
   determine species given unknown sequence
   
6. 
   guess likely function of gene using homology searches
   
7. 
   assess variation at the Mc1r gene in vertebrates
   
8. 
   use sub-routines to infer mutation type in a protein sequence
   
9. 
   what primate species has the fastest evolving Foxp2 gene?
   
10. 
    compare hash- and array-based scripts on computer time taken
    
11. 
    determine origin of unknown high-throughput sequence library.
    
12. 
    incorporate simple BioPerl/CPAN module to execute homology searches