[109-2] Asia University, Bioinformatics – assignment

Student ID: 109712242 Name: Siti Nurhikmah Maulidia Rinjani(50 points total)
Point your browser to NCBI home page.
1. What are the Genbank common name of the following species ?
a. Acer rubrum common name: Red mapple (5 points)
b. Orycteropus afer common name: Aadvark (5 points)
Hint : point your browser to NCBI home page and use Taxonomy to search.
2. Point your browser to NCBI PubMed home page [https://pubmed.ncbi.nlm.nih.gov/]. Using the keyword
SARS-CoV2[TI], I found 400 publications have the title “SARS-CoV2” dated on 2021/3/13.

Using the same keyword “SARS-CoV2[TI]” as input, how many items you found? 403 items
(5 points)

Print the date you perform the keyword search. Date : March 17, 2021 (5 points)
How many items are published by the author with last name ‘Ng’? 8449 items. (5 points)
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How many items are published by the author with last name and initials KL; ‘Ng KL’? 0 items. (5 points)

3. Retrieve the following three protein sequences in FASTA format: a. horse pancreatic ribonuclease [Equus
caballus (horse) P00674], b. minke whale pancreatic ribonuclease [Balaena rostrata (Common minke
whale)] & c. kagaroo pancreatic ribonuclease [Macropus rufus (Red kangaroo)] [Hint: Use pancreatic
ribonuclease as your keyword to search the UniProt https://www.uniprot.org/ home page. You may find
more than one sequence for each species. Fill in the details for the protein, pancreatic ribonuclease, in the
table below. (12 points)

Species Horse Minke whale Kangaroo

Primary Accession ID P00674 P00673 P00686
Length of Amino acids 128 124 122
Molecular weight 14,374 14,125 13,832
Number of 26-84 26-84 25-83
DISULFID bond 40- 95 40-95 39-94
58-110 58-110 57-109
65-72 65-72 64-71

4. Using the three sequences from question 4 to determine which two of these species are most closely
related by doing multiple sequence alignment (MSA). [Hint: Point your browser to the Clustal Omega
https://www.ebi.ac.uk/Tools/msa/clustalo/ web site and perform the MSA alignment. Then, from the
phylogenetic tree result, determine which two species are most closely related. A smaller evolution
distance implies they are closer.] (8 points)
A. horse and minke whale are most closely related
B. horse and kangaroo are most closely related
C.kangaroo and minke whale are most closely related
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Answer:

A (with protein in step 1)

C (with RNA in step 1