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.
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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.
