Question

1.The procedure used to align many sequences at the same time is called: *

• diversity sequence alignment
• multiple sequence alignment
• local alignment
• multiple statistical alignment
• substitution matrix alignment

2.The method of alignment that tries to align regions with high level matches without considering the alignment of the rest of the sequence is called: *

• global alignment
• multiple sequence alignment
• local alignment
• multiple statistical alignment
• high level matching alignment

3.The type of sequence alignments that is most suited for finding conserved patterns in DNA or protein sequences is called: *

• global alignment / multiple sequence alignment
• local multiple alignment
• local alignment / multiple polymorphism search
• multiple statistical alignment
• high level matching alignment

4. An outbreak of pneumonia has occurred. This outbreak appears to involve a family who had attended a family gathering and wedding ceremony. The samples from the patients were then tested by PCR using the primers for 16S rRNA and RT-PCR using primers for SARS and SARS-CoV-2 coronaviruses. Select statements that are TRUE pertaining to the case involving this family. The sequence of the amplified fragment from the PCR is provided here: AACACGGAGAGTTTGATCCTGGCTCAGAACTAACGCTGGCGGCGCGTCTTAAACATGCAAGTCAAGCGGAGTAGCAATACTCAGCGGCGAACGGGTGAGTAACACGTGGGTAATCTTCCTCTGAGTCTGGGATAACTTTCCGAAAGGGAAGCTAATACTGGATGGTCCCGAGAGATCACAAGATTTTTCGGGTAAAGATTTATTGCTCGGAGATGAGCCCGCGTCCGATTAGCTAGTTGGTGAGGTAAAGGCTCACCAAGGCGACGATCGGTAGCCGGCCTGAGAGGGTGTTCGGCCACAATGGAACTGAGACACGGTCC ATACTCCTACGGGAGGCAGCAGTTAAGAATCTTGCTCAATGGGGGGAACCTGAAGCAGCGACGCCGCGTGAACGATGAAGGTCTTCGGATTGTAAAGTTCAGTAAGCAGGGAAAAATAAGCAGCAATGTGATGATGGTACCTGCCTAAAGCCACCGGCTAACTACGTGCCAGCAGCCGCGGTAAAACGTATGGTGCAAGCGTTGTTCGGAATCATTGGGCGTAAAGGGTGCGTAGGCGGACATGTAAGTCAGGTGTGAAAACTGCGGGCTCAACTCGCAGCCTGCACTTGAAACTATGTGTCTGGAGTTTGGGAGAGGCAAGTGGAATTCCAGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCAGTGGCGAAGGCGACTTGCTGGCCTAAAACTGACCCTGAGGCACGAAAGCGTGGGTAGTGAACGGGATTAGATACCCCGGTAATCCACGCCCTAAACGTTGTCTACCAGTTGTTGGGGGTTTTAACCCTCAGTAACGAACCTAACGGATTAAGTAGACCGCCTGGGGACTATGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGTCCGCACAAGCGGTGGAGCATGGTGGTTTAATTCGATGATACGCGAAAAACCTCACCTAG GCTTGACATGGAGTGGAATCATGTAGAGATACATGAGCCTTCGGGCCGCTTCACAGTTGCTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCACCTTATGTTGCCATCATTCAGTTGGGCACTCGTAAGGAACTGCCGGTGACAAACCGGAGGAAGGCGGGGATGACGTCAAATCCTCATGGCCTTTATGTCTAGGGCAACACACG *

• The pathogen is a type of coronavirus.
• The physician can inform the family that they are suffering from a disease called leptospirosis.
• The patients should be quarantined because they have COVID-19
• The pneumonia is due to a bacterial infection.
• The pneumonia can be treated with antibiotics.

5.Your research group has just completed the genome sequencing for a new bacterial species named V. novela. This newly sequenced genome has not yet been annotated. Your colleague has been studying the VTOX protein in E. modeli for many years and is interested in finding out whether a homolog for the VTOX protein can be found in the bacterial species V. novela. Select the options that are TRUE that can be used to provide an answer to your colleague.

• Do a blastn against the PDB database.
• Use the blastp program with the VTOX protein as the query to search the UniProt database.
• Use the VTOX protein sequence as a query for the tblastn program to search the V. novela genome as the database.
• Search the E. modeli database using tblastn and the VTOX protein as the query.
• Carry out a gene prediction for the V. novela genome and use the resulting genes as blastx queries to search a protein sequence database.

Answer 1

Question number 1.

Answer: Multiple sequence alignment.

Explanation:

Multiple sequence alignment is a type of sequence alignment in which two or more sequences can be aligned at the same time to analyze the evolutionary relationship between them.

Question number 2:

Answer: Local alignment.

Explanation:

In local alignment the local regions of similarity will be identified rather than aligning the entire length of the sequence. This technique is most widely used for aligning dissimilar sequences which are suspected to have regions that are very similar like sequence motifs.

Question 3:

Answer: Local alignment / multiple polymorphism search

Explanation:

The multiple sequence alignment and global alignment consider aligning the entire length of the sequence and it will be scored based on the matches, mismatches and gaps in the alignment. On the other hand, local alignment identify local regions of similarity between two sequences.