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    Assig Nmen T5: International University Bioinformatics

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    Trang Minh
    This document contains the assignment report from a group of bioinformatics students. It includes: - The names and student IDs of the group members. - Four questions regarding analyzing amino acid frequencies, phylogenetic tree construction, and comparing trees. - For each question, the group reported their findings in point form or paragraphs, including the frequency of certain amino acids in different species, which species are most and least closely related to humans based on amino acid distances, groups in the NJ tree supported by bootstrap values over 50%, and a comparison of the topologies and branch lengths between the NJ and ML trees.

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    Assig Nmen T5: International University Bioinformatics

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    Trang Minh
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    This document contains the assignment report from a group of bioinformatics students. It includes: - The names and student IDs of the group members. - Four questions regarding analyzing amino acid frequencies, phylogenetic tree construction, and comparing trees. - For each question, the group reported their findings in point form or paragraphs, including the frequency of certain amino acids in different species, which species are most and least closely related to humans based on amino acid distances, groups in the NJ tree supported by bootstrap values over 50%, and a comparison of the topologies and branch lengths between the NJ and ML trees.

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    Bioinfo-Assignment5-Group6-official

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    This document contains the assignment report from a group of bioinformatics students. It includes: - The names and student IDs of the group members. - Four questions regarding analyzing amino acid frequencies, phylogenetic tree construction, and comparing trees. - For each question, the group reported their findings in point form or paragraphs, including the frequency of certain amino acids in different species, which species are most and least closely related to humans based on amino acid distances, groups in the NJ tree supported by bootstrap values over 50%, and a comparison of the topologies and branch lengths between the NJ and ML trees.

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    49 views6 pages

    Assig Nmen T5: International University Bioinformatics

    Uploaded by

    Trang Minh
    This document contains the assignment report from a group of bioinformatics students. It includes: - The names and student IDs of the group members. - Four questions regarding analyzing amino acid frequencies, phylogenetic tree construction, and comparing trees. - For each question, the group reported their findings in point form or paragraphs, including the frequency of certain amino acids in different species, which species are most and least closely related to humans based on amino acid distances, groups in the NJ tree supported by bootstrap values over 50%, and a comparison of the topologies and branch lengths between the NJ and ML trees.

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    of 6

    INTERNATIONAL UNIVERSITY

    BIOINFORMATICS

    ASSIG
    NMEN
    T5
    Group’s member: Nguyễn Thị Mỹ Yến - BTBTIU18355
    Đỗ Thụy Hồng Nhung - BTBTIU18185
    Hoàng Nguyễn Minh Châu - BTBTIU18374
    Nguyễn Huỳnh Thùy Trang - BTBTIU16139
    Course: Bioinformatics
    Lecturer : Dr. Nguyen Minh Thanh

    1
    Question 1: Report frequency (%) of the following amino acids:  
    a. Ala of Pan troglodytes (Chimpanzee) & Macropus robustus (Kangaroo)  
    _ Ala of Pan troglodytes (Chimpanzee): 8.20 % 
    _ Ala of Macropus robustus (Kangaroo): 8.23% 
    b. Met of Homo sapiens (Human) & Mus musculus (Mouse) 
    _ Met of Homo sapiens (Human): 1.41% 
    _ Met of Mus musculus (Mouse): 1.01 % 
    c. Gly of Gorilla gorilla (Gorilla): 9.22% 

    Questions 2: Based on the pairwise distances for amino acids, report:

    a. Which species is the closest relative of human?

    b. Which species is the most distant relative of human?

    Most Distant

    Closest

    a. Which species is the closest relative of human?


    According to the p-distance, the p-distance between chimpanzee and human is the
    smallest (0.0203). Hence, the closest relative of human here is chimpanzee.

    b. Which species is the most distant relative of human?


    Observing the p-distance between crodile and human which is the largest p-distance
    compared with p-distance of human and other species. This indicates the crodile and
    human have the most distant relation.

    Question 3: Which groups in the NJ tree have Bootstrap support value >50%?

    2
    3
     Pan troglodytes (Chimpanzee), Homo sapiens (Human): 94%

     Pan troglodytes (Chimpanzee), Homo sapiens (Human), Gorilla gorilla


    (Gorilla): 100%
     Pan troglodytes (Chimpanzee), Homo sapiens (Human), Gorilla gorilla
    (Gorilla), Papio hamadryas (Baboon): 100%
     Hyla japonica (Frog), Crocodylus johnsoni (Crocodile): 58%
     Hyla japonica (Frog), Crocodylus johnsoni (Crocodile), Pomacanthus
    imperator (Angelfish): 85%

    Questions 4: Compare the NJ and ML trees:

    4
    5
    a. Do two trees have the same topology?
    No, they do not have the same topology
    b. Report the sum of branch length for each tree.
    Neighbor-Joining Tree: 1.21778294
    Maximum-likelihood tree: 1.74743661
    c. Identify two groups that are well supported in all of two trees.
    1. Pan troglodytes (Chimpanzee), Homo sapiens (Human), Gorilla gorilla (Gorilla)
    2. Pan troglodytes (Chimpanzee), Homo sapiens (Human), Gorilla gorilla (Gorilla),
    Papio hamadryas (Baboon).

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