Bioinformatics: Human Genome Databases – Ensembl Genome Browser- Bioinformatics Assignment Help

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Bioinformatics Assignment Help:

Task:

You will be allocated one gene from the list:?See the allocation list on the BlackBoard site. In addition:
> Undergraduate students (ONPS2093) will be allocated two rare SNP for their gene. > Postgraduate students (ONPS2639) will be allocated four rare SNPs for their gene.

Four activities will be carried out for the assignment:

1. Obtain the exon / intron structure of the gene.
2. Investigate the rare homozygous SNPs for the patient.
3. Find the other single nucleotide polymorphisms (SNPs) within this gene.
4. Design PCR primers for the rare homozygous SNPs using a primer design program.

ACTIVITY 1: Obtain the exon / intron structure of the gene

Questions:

1. select the most appropriate gene transcript and determine the number of exons and introns in the gene transcript.

2. provide a diagram showing the structural arrangement of exons and introns throughout the gene transcript.

3. also indicate how many transcripts are present for your gene. Use the following genome browser: ?Ensembl?http://asia.ensembl.org/index.html

An Ensembl Handbook can be found on the BlackBoard site. This is your main resource for the assignment. ?In addition several tutorials for the Ensembl website can be found on this link: ?http://asia.ensembl.org/info/website/tutorials/index.html ?> see the tutorials listed under “Using the Ensembl genome browser”

ACTIVITY 2: Investigate the rare homozygous SNPs for the patient Access the Ensembl websites and identify the rare homozygous SNPs that were ?provided for your gene (patient data). ?Questions:

1. Which area of the gene are the SNPs located? (exon, intron, etc).

2. Do they change the coding region?

3. What potential effect, in any, do the SNPs have on the final protein? Use the ?Variant EffectPredictor?Ensembl?http://www.ensembl.org/Homo_sapiens/Info/Index http://asia.ensembl.org/info/genome/variation/index.html ?Variant Effect Predictor ?http://asia.ensembl.org/Homo_sapiens/Tools/VEP

 

ACTIVITY 3: Find the other single nucleotide polymorphisms (SNPs) within this gene

Questions:

1. Provide a summary of the SNPs for the gene.

2. Determine how many SNPs are in the exons and introns.

3. Are there any exons which have a greater proportion of SNPs, or are they ?randomly distributed??Use the Ensembl websites and Handbook, as listed under Activity 2.

ACTIVITY 4: Design PCR primers for the rare homozygous SNPs using a primer design program ?You will need to download the DNA sequence surrounding your rare homozygous SNPs for your gene and save it as a file (see Activity 2). Undergraduate students have two rare SNP, postgraduate students should use the four SNPs that were allocated. Approximately 300 bases either side of the SNP will be sufficient (~ 600 bases in total). ?You should design PCR primers to the rare homozygous SNPs using a PCR primer design program. ?The program is “Primer3” which has been developed by the Whitehead Institute for Biomedical Research (Boston). Go to the following website; ?http://frodo.wi.mit.edu/primer3/input.htm ?Copy and paste the DNA sequence into the main box; examine the options and pick the primers. Repeat with the second rare homozygous SNP from the gene (postgraduate students are given 4 rare SNPs).

Question:

• List the forward and reverse primers from the 5’ to 3’ end that you have selected for the rare SNP(s).

Uploaded By : jack
Posted on : April 07th, 2018
Downloads : 1

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