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MB5021 Bioinformatics

Please answer the following questions for your laboratory write up. You should use the information that you’ve learnt in both the lectures and the laboratory session, as well as information you’ve gained from further reading.

You should write approximately 100 words for each written answer but exact word counts are not needed. References are not needed but can be added to demonstrate further reading.

  1. Discuss what steps are employed to improve the quality of the filtered reads compared to the raw reads and how this is assessed using FastQC reports.  
  2. Including an explanation of short read sequencing chemistries, discuss why errors and poor quality bases may arise, and why it is important to quality filter sequencing reads.
  3. Produce the suffix array for the following sequences. Include your workings in your answers:
  4. a) ATCGTCGGAT
  5. b) GGCACGTACA
  6. Produce the BWT for the following sequences. Include your workings in your answers:
  7. a) ATCGTCGGAT
  8. b) GGCACGTACA
  9. List two downstream applications of sequence alignments and discuss the challenges faced during alignment.
  10. Using the results from Variant Effect Predictor, list the different consequences a sequence variant may have on both the DNA sequence and the protein and discuss the impact variants can have on the phenotype of an individual.

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