In this exercise, we will examine the DNA sequencing data from your saliva sample using common, mostly web-based bioinformatics tools.
1. Open and inspect your sequence trace with 4Peaks. Click on the spoke in the bottom left corner of 4peaks and copy the sequence.
2. From the links page of the course website, select the Pairwise sequence alignments link.
3. Click on the Needle link on the EMBL website. Paste your sequence in the top box and the reference sequence in the bottom box.
4. Using Needle, align your sequence to the reference sequence – are there any mismatches outside of the messy regions at the ends?
5. From the links page of the course website, select the TCoffee link and align your sequence to the reference sequence. Your sequence and the reference sequence should be pasted in fasta format.
6. What would happen if the allele was heterozygous? How can you check? Check each of the 5 SNP positions to determine if it's heterozygous by copying ~15 nt upstream of the SNP and searching it in 4peaks.
7. From the links page of the course website, select the BLAST link and blast your sequence against the human genome.
8. What are the top two hits? Ignore the tubular (TUBB3) hit as it is antisense to the gene we're interested in. Does your allele match the BLAST reference genome sequence?
9. Do a google search and identify the function of the gene and a common physical trait variation in the gene is associated with (it's something easily recognized). The wiki page for the gene is a good starting point.
10. Answer the following questions and submit your answers on Canvas: