BME355: Imagine You have been Assigned the Task of Determining the Functional Importance: Genomic Sequence Analysis Assignment, SUSS, Singapore

Question 1

Imagine you have been assigned the task of determining the functional importance of the human ACE2 gene. Investigate and furnish answers to the following questions:

• Provide the full name of the gene and the chromosome it is found on.
• Discuss the function of this gene.
• List the pathways this gene is involved in.

Question 2

Examine the following statements and critically evaluate their accuracy. The answer to each question should not be more than 300 words.

• Protein alignments are often more informative than DNA alignments.
• It is never correct to say that two sequences share a certain percentage of homology.
• When comparing two sequences, it may be necessary to repeat the search using different scoring matrices.
• 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 determine their accuracy.

Question 3

Analyze the Conserved Domain Database (CDD) identifier cd03683 to solve the following questions:

• Determine the protein family the CDD identifier represents. What are the functions of the protein family?
• Identify conserved features or sites.
• Obtain FIVE (5) representative protein sequences in FASTA format and conduct a multiple sequence alignment. (Paste the screenshot of the MSA generated).
• Evaluate the multiple sequence alignment generated.

Question 4

Analyze the given sequence using bioinformatics tools and answer the following questions:

>testseq

MALFVRLLALALALALGPAATLAGPAKSPYQLVLQHSRLR

GRQHGPNVCAVQKVIGTNRKYFTNCKQWYQRKICGKSTVI

SYECCPGYEKVPGEKGCPAALPLSNLYETLGVVGSTTTQLY

TDRTEKLRPEMEGPGSFTIFAPSNEAWASLPAEVLDSLVSN

VNIELLNALRYHMVGRRVLTDELKHGMTLTSMYQNSNIQIH

HYPNGIVTVNCARLLKADHHATNGVVHLIDKVISTITNNIQQ

IIEIEDTFETLRAAVAASGLNTMLEGNGQYTLLAPTNEAFEK

IPSETLNRILGDPEALRDLLNNHILKSAMCAEAIVAGLSVET

LEGTTLEVGCSGDMLTINGKAIISNKDILATNGVIHYIDELLI

PDSAKTLFELAAESDVSTAIDLFRQAGLGNHLSGSERLTLL

• Solve the identity of the sequence and the organism it belongs to. Using screenshots list out the steps used to determine its identity.
• Determine the function of the sequence and the conserved domains present in it.
• List out the Gene Ontology processes and the pathways its corresponding gene is involved in.

Question 5

Answer the following questions in your own words. The answer to each question should not be more than 300 words.

• Evaluate the difference between Local and Global alignments.
• Describe the BLAST algorithm.
• Evaluate how the statistical significance of a BLAST search result is assessed through E-values.
• Demonstrate the practical applications of multiple sequence alignments.