Goal

This practical introduces you through several online databases and tools used in Bioinformatics, such as Blast and Expasy

Excercise 1: Using BLAST

Goal:

Use Blast. Identify the Gene in a Sleep Disorder, exercise from https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/q_mastery_blastn_blastp.html

  1. Copy the sequence from above link.
  2. Go to Blast: https://blast.ncbi.nlm.nih.gov/Blast.cgi
  3. Perform a Nucleotide Blast using the DNA sequence
  4. Perform a protein Blast using the Amino Acid sequence
  5. What gene correlates with the sleeping disorder?
  6. Is there difference in the number in resulting hits in the databases between nucleotides and proteins? Which one would be more specific?

Excercise 2: From DNA to Protein!

Goal:

Learn about open reading frames, from DNA to Protein!

  1. Copy the sample DNA sequence from https://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/InfoHubs/infohubs3.html
  2. Go to Blast: what is the gene name associated?
  3. Google: what is the clinical relevance of this gene (i.e. in health care) ?
  4. Do a blastx, find the amino acid sequence, and download it in the FASTA format.
  5. Download the FASTA format of the gene.
  6. Every nucleotide sequence can be read in 6 reading frames: every 3 nucleotides can be translated in 1 amino acid, and DNA can be read 5’ –> 3’ or 3’ –> 5’. Parts that start with Met and and with Stop are translated into amino acids. We want to find out: What is the reading frame for this protein? To find out, go to Expasy: https://web.expasy.org/translate/
  7. Type in the DNA sequence from the FASTA file
  8. Take notice: “Open reading frames are highlighted in red. Please select one of the following frames - in the next page, you will be able to select your initiator and retrieve your amino acid sequence:” The protein code you saved earlier is one of the ORFs.
  9. and find out: what is the reading frame for this protein?
  10. Take note in the Translate tool: “Open reading frames are highlighted in red. Please select one of the “Methionine” or one of the highlighted residues following a Stop codon (or the beginning of the sequence).”

Excercise 3: Learn about genes!

Goal:

How do you find out information about genes online?

In Prof Simon E. Fisher’s Twitter thread he talks the about the ORIG3N Superhero consumer DNA test, writing “They claim their FOXP2 test can reveal whether “you have the mind of a super-genius”. [Bangs head repeatedly against desk while sobbing.]”

  1. Which genes are included in the Superhero test at https://shop.orig3n.com/products/superhero ?
  2. Go to https://www.ncbi.nlm.nih.gov
  3. What can you learn about the genes? Can you find evidence for superhuman ability in the FOXP2 gene? What about the other genes mentioned in the Superhero test?

Other interesting software in bioinformatics:

  • Jalview is used to align sequences. You can download them in the FASTA format, and import them in Jalview.

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