BME355 Genomic Sequence Analysis ECA Assignment, SUSS, Singapore Demonstrate your understanding in the basic concepts of molecular genetics by critically evaluating the following statements
Demonstrate your understanding in the basic concepts of molecular genetics by critically evaluating the following statements:
The statistical significance of a BLAST result can be assessed through E-values.
When comparing two sequences, it may be necessary to repeat the search using different scoring matrices.
Protein alignments are often more informative than DNA alignments.
Position-specific iterated BLAST (PSI-BLAST) is often more sensitive than a regular BLAST search in finding distantly related protein sequences.
Benchmarking is an important approach to compare different software and to determine their accuracy.
You have been assigned the task of determining the functional importance of the human CFTR gene. Investigate and solve the following questions:
List the full name and gene ID of this gene and the RefSeq IDs of its corresponding mRNA and protein.
State the chromosome in which the human CFTR gene is found on, and in the tissues where it shows high expression.
Discuss the function of this gene.
Using the Molecular Signatures Database (MSigDB) information for Fatty Acid
Metabolism assemble the following tasks:
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).
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.
Appraise the results obtained and discuss how relevant the findings are to the gene list.
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.
Attach the sequences in fasta format.
Create a multiple sequence alignment using any multiple sequence alignment tool and attach the alignment and the phylogenetic tree.
Evaluate the alignment and the phylogenetic tree derived from the alignment.
With the help of an alignment tool you have learnt, investigate the given human sequence and furnish answers to the following questions:
Determine the name and accession number of the sequence.
Identify the conserved domains/features in this sequence.
State the superfamily in which the sequence belongs to. Discuss its functional role.
List FIVE (5) pathways its genic form is involved in.
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