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.