|University||Singapore University of Social Science (SUSS)|
|Subject||BME355 Genomic Sequence Analysis Assignment|
BME355 Genomic Sequence Analysis Assignment, SUSS, Singapore: Using the OMIM database information for Type 2 Diabetes Mellitus (T2D)
Using the OMIM database information for Type 2 Diabetes Mellitus (T2D)
(https://omim.org/entry/125853), solve the following tasks.
Extract out the genes associated with T2D and use the list as input in the online tool DAVID (Database for Annotation, Visualization, and Integrated Discovery).
Create a functional annotation clustering of the gene list and paste screenshots of the results from GOTERM_BP/CC/MF_DIRECT and KEGG_PATHWAY. Report the clusters having enrichment scores above 1.
Appraise the results obtained and discuss the relevancy of the findings to the gene list.
Using the NCBI database, explore the gene with Gene ID: 79923.
State the gene symbol given to this ID and the full official name of the gene.
Discuss the function of this gene in your own words.
Determine the mRNA transcripts and protein isoforms of this gene.
Describe FIVE (5) pathways in which the corresponding gene is involved in.
Identify the conserved domains in the protein isoforms of this gene.
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Demonstrate your understanding of molecular genetics and computational biology by critically evaluating the following statements.
Protein alignments are often more informative than DNA alignments.
When comparing two sequences, it is necessary to repeat the search using different scoring matrices.
The statistical significance of a BLAST result can be assessed through S-values.
Position-specific iterated BLAST (PSI-Blast) is often less sensitive than a regular Blast search in finding distantly related protein sequences.
Benchmarking is an important approach to compare different software and determine their accuracy.
With the help of an alignment tool you have learned, examine the human sequence given below, and furnish answers to the following questions:
Give the name and accession number of the sequence.
Appraise the function of the corresponding gene.
Describe FIVE (5) pathways which the genic form is involved in.
List the Gene Ontology functions and processes.
Using the resulting information from the above-mentioned sequence in
extract out the sequences from Homo sapiens and organisms such as Pan troglodytes, Canis lupus familiaris, Bos Taurus, and Mus musculus
Paste the sequences in a fast format.
Create a multiple sequence alignment using any multiple sequence alignment tool. Paste the alignment and the phylogenetic tree.
Evaluate the alignment and the phylogenetic tree derived in Question 5b.
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