Question 1
Demonstrate your understanding in the basic concepts of molecular genetics by critically evaluating the following statements:
Question 1a
The statistical significance of a BLAST result can be assessed through E-values.
Question 1b
When comparing two sequences, it may be necessary to repeat the search using different scoring matrices.
Question 1c
Protein alignments are often more informative than DNA alignments.
Question 1d
Position-specific iterated BLAST (PSI-BLAST) is often more sensitive than a regular BLAST search in finding distantly related protein sequences.
Question 1e
Benchmarking is an important approach to compare different software and to determine their accuracy.
Question 2
You have been assigned the task of determining the functional importance of the human CFTR gene. Investigate and solve the following questions:
Question 2a
List the full name and gene ID of this gene and the RefSeq IDs of its corresponding mRNA and protein.
Question 2b
State the chromosome in which the human CFTR gene is found on, and in the tissues where it shows high expression.
Question 2c
Discuss the function of this gene.
Question 3
Using the Molecular Signatures Database (MSigDB) information for Fatty Acid
Metabolism assemble the following tasks:
Question 3a
Pull out the 158 genes involved in the metabolism of fatty acids, and use the list as input in the online tool DAVID (Database for Annotation, Visualization and Integrated Discovery).
Question 3b
Perform a functional annotation clustering of the gene list by only selecting the following: GOTERM_BP/CC/MF_DIRECT, REACTOME_PATHWAY and
KEGG_PATHWAY. Attach a screenshot of the top THREE (3) annotation clusters on the basis of the enrichment score.
Question 3c
Appraise the results obtained and discuss how relevant the findings are to the gene list.
Question 4
Using the NCBI’s HomoloGene resource and the ID: 4349, obtain sequences (one each) from Human and organisms such as B. taurus, M. musculus, D. rerio, C. elegans.
Question 4a
Attach the sequences in fasta format.
Question 4b
Create a multiple sequence alignment using any multiple sequence alignment tool and attach the alignment and the phylogenetic tree.
Question 4c
Evaluate the alignment and the phylogenetic tree derived from the alignment.
Question 5
With the help of an alignment tool you have learnt, investigate the given human sequence and furnish answers to the following questions:
SEQ
MKWVWALLLLAALGSGRAERDCRVSSFRVKENFDKARFSGTWYAMAKKDP
EGLFLQDNIVAEFSVDETGQ
MSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGN
DDHWIVDTDYDTYAVQYSCR
LLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYC
DGRSERNLL
Question 5a
Determine the name and accession number of the sequence.
Question 5b
Identify the conserved domains/features in this sequence.
Question 5c
State the superfamily in which the sequence belongs to. Discuss its functional role.
Question 5d
List FIVE (5) pathways its genic form is involved in.
