Perl Programming Course for Bioinformatics and Internet

Final Assignment( tips, grading criteria )
Students are expected to work on this assignment on their own, not in pairs.
Objective:
To create a search engine to retrieve info on genes present on Saccharomyces cerevisiae's chromosome IV.
Source files location:
All the files you need are located in ../sources/yeastGenome, if accessed from your home directory on bicourse.
You may also retrieve the files from yeastGenome
Task:
  1. Parse the file yeast_chromosome_IV.genbank
  2. For each gene get from from the file the gene name, locus, start and end position. Ignore the genes marked by "complement"
  3. Store the retrieved data in a hash like structured file with YAML::Any or Data::Dumper.
  4. Provide a GUI (Graphic User Interface) and allow to search this data by gene and locus name, and by position in the chromosome. Return meaningful messages when the requested name or position is unknown or invalid.
  5. Display gene, locus, start-end, sequence, translated sequence and recent publications for the requested gene.
    • Retrieve the sequence and translated sequence from the locus.genbank file in directory chromosome_IV.
    • Retrieve the list of recent publications from sqfbin/recentReferences?d=240&c=prg&seq=SEQ
      passing the translated sequence (no spaces) as parameter, as in this .
      NOTE for the purpose of this course, please use recentReferencesLite as in this .
Perl modules to use:
  1. CGI
  2. YAML::Any or Data::Dumper
  3. LWP::Simple

Dr Jaime Prilusky, course@weizmann.ac.il.