PHAR5350 – Bioinformatics Assignment – De Montfort University, UK
All Tasks must be performed INDEPENDENTLY. You should perform the two mini projects and submit them as a single Word document or pdf containing your results.
Part A – Dr Webb
Task 1 – Halothane is an inhaled anaesthetic used for general anaesthesia.
i. Interrogate the PharmGKB database for pharmacogenes associated with Halothane. List the genes you identify and the first variation for each gene.
ii. Use the GWAS catalog to determine if the gene /s you listed in 1a have been associated with a phenotypic response in genome wide association studies. Present your results and then identify any variations relevant to Halothane or its adverse effects.
iii. Produce a summary table for each of the SNPs you have identified in 1a and 1b from their dbSNP entries, (this should include comment on any population diversity information that is available).
Task 2 – Investigate the small nucleotide polymorphisms database (dbSNP) for variations in the gene /s you identified in question 1a.
For each gene:
a. How many variations are present in total?
b. How many variations are located in the coding region?
c. How many variations are nonsynonymous?
d. How many variations are pathogenic?
i. Create a table that catalogues the information you have collected to answer the above questions.
For the first pathogenic variation / s you identified in 2a access the variation viewer view of ~ 1000 bases of it in the GRCh38.p12 assembly (annotation release 109).
ii. For each gene variation create a table that catalogues the variation type and the molecular consequences of the variations in this region.
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Task 3 – Using the genome variation server, identify tag SNPs for a gene you identified in question 1a that are located within 10,000 bases upstream and downstream of the gene and are common to the all the HAPMAP panels and a r2 value of 0.8 and an allele frequency of 20%. Provide answers to the following questions:
i. How many Tag SNPs are common to all these populations?
ii. Identify the Tag SNPs need to cover this region of the genome for all the populations
iii. Which population group / s requires the highest and lowest number of Tag SNPS to cover the region?
iv. Repeat the analysis with the r2 at 0.8 and allele frequency altered to 10%. Describe the effect this change has on the results and explain why it does so.
Task 4 – You are required to design a test to identify individuals who are at risk of malignant hyperthermia when using volatile anaesthetics such as halothane.
i. Consider the variations you have identified for question 1 and 2. Discuss which would you include in the test?
ii. Perform a literature search to identify additional variations for inclusion.
iii. Provide a critical evaluation of whether there are any population groups that the test results would be most beneficial for?
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Part B – Dr Smith
Sequence –
MSALCWGRGAAGLKRALRPCGRPGLPGKEGTAGGVCGPRRSSSASPQEQDQDRRKDWGHV
ELLEVLQARVRQLQAESVSEVVVNRVDVARLPECGSGDGSLQPPRKVQMGAKDATPVPCG
RWAKILEKDKRTQQMRMQRLKAKLQMPFQSGEFKALTRRLQVEPRLLSKQMAGCLEDCTR
QAPESPWEEQLAQLLQEAPGKLSLDVEQAPSGQHSQAQLSGQQQRLLAFFKCCLLTDQLP
LAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYA
AALQCMGRQDQDAGTIERCLEQMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSL
PPQLPPPVNTSKLLRDVYAKDGRVSYPKLHLPLKTLQCLFEKQLHMELASRVCVVSVEKP
TLPSKEVKHARKTLKTLRDQWEKALCRALRETKNRLEREVYEGRFSLYPFLCLLDEREVV
RMLLQVLQALPAQGESFTTLARELSARTFSRHVVQRQRVSGQVQALQNHYRKYLCLLASD
AEVPEPCLPRQYWEALGAPEALREQPWPLPVQMELGKLLAEMLVQATQMPCSLDKPHHSS
RLVPVLYHVYSFRNVQQIGILKPHPAYVQLLEKAAEPTLTFEAVDVPMLCPPLPWTSPHS
GAFLLSPTKLMRTVEGATQHQELLETCPPTALHGALDALTQLGNCAWRVNGRVLDLVLQL
FQAKGCPQLGVPAPPSEAPQPPEAHLPHSAAPARKAELRRELAHCQKVAREMHSLRAEAL
YRLSLAQHLRDRVFWLPHNMDFRGRTYPCPPHFNHLGSDVARALLEFAQGRPLGPHGLDW
LKIHLVNLTGLKKREPLRKRLAFAEEVMDDILDSADQPLTGRKWWMGAEEPWQTLACCME
VANAVRASDPAAYVSHLPVHQDGSCNGLQHYAALGRDSVGAASVNLEPSDVPQDVYSGVA
AQVEVFRRQDAQRGMRVAQVLEGFITRKVVKQTVMTVVYGVTRYGGRLQIEKRLRELSDF
PQEFVWEASHYLVRQVFKSLQEMFSGTRAIQHWLTESARLISHMGSVVEWVTPLGVPVIQ
PYRLDSKVKQIGGGIQSITYTHNGDISRKPNTRKQKNGFPPNFIHSLDSSHMMLTALHCY
RKGLTFVSVHDCYWTHAADVSVMNQVCREQFVRLHSEPILQDLSRFLVKRFCSEPQKILE
ASQLKETLQAVPKPGAFDLEQVKRSTYFFS
Task 1 – You have been provided with a sequence of a human protein (above).
i) Identify what the sequence is and discuss its function.
ii) Prepare a multiple sequence alignment of sequence 1 with other similar sequences in different organisms.
iii) Using your multiple sequence alignment, produce a phylogenetic tree. In your answer, consider adding an outlier to help with rooting. Discuss your findings.
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Task 2 – The next tasks are centred around the human cytochrome P450 genes, with particular focus on CYP2E1.
i) Determine the phylogenetic relationships between members of the human CYP2 family. In your answer, you should consider the below points:
a. Search strategy for genes in the human CYP2 family
b. Multiple alignment of CYP2 sequences
c. Optimisation of alignment, if required
d. Selection of alignment regions for phylogenetic analysis
e. Phylogenetic analysis using suitable method(s)
f. Visualisation of the phylogeny as a phylogenetic tree
ii) Compare the two following studies of gene expression profiles in normal human tissues on the NCBI GEO site. In your comparison, discuss the experimental design and consider the platforms and the number and range of samples used.
a. Series GSE7905
b. Series GSE2361
iii) Determine the expression profile of CYP2E1 in normal human tissues using the above two series.
a. In which tissue is CYP2E1 expression most prominent?
b. How similar are the results from the two studies?
iv) Compare and discuss the expression profile of CYP2E1 from these two studies with that shown in the 53 GTEx RNA-Seq study in the EBI Gene Expression Atlas.
a. Based on what you know of its function, are these results to be expected
