Sequence Characteristics in Genes Exercise 1

Exercise 1 - Characteristics of Genic vs. Non-Genic DNA

The nucleotide composition and sequence in genes differ from those in intergenic regions. Gene prediction tools utilize these differences to separate regions that are likely to contain genes from non-coding, intergenic regions. During this exercise you will detect differences in nucleotide composition between genic and intergenic DNA.


• Each group is assigned a sequence set of three sequences from intergenic, genic, or random sequences. Determine for your each sequence in your assigned set the nucleotide composition and compare the results across the different sequence types.
  
  
  • Access your sequence set here:   #1,   #2,   #3,   #4,   #5,   #6,   #7,   #8,   #9,   #10,   #11,   #12.
  • Highlight and copy a nucleotide sequence.
  • Paste sequence into this sequence calculator. (This tool is still under development. Should you experience difficulties use 'Sequence Stats' from the DNALC Sequence Utilities.)
  • Select 'Stats'.
  • Move the sequence bin onto the tool.
  • Select 'Single element' mode.
  • Transfer results into appropriate columns in this worksheet.
  • Select 'Pairs' mode.
  • Transfer results into appropriate columns in the worksheet.
  • Repeat this analysis for the next two sequences.
  • Determine the average for the three sequences.
  • Get together with the team that has worked on sequences of the same type as you and average the results of the two teams.
  • Enter your results into the course database (table on board or presenter computer).

• Compare the data for the different sequence types and identify significant differences.

• How could these differences aid in gene identification?