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    Bioinformatics Assignment 1: Accessing Ncbi Databases: International University - Vnu HCMC School of Biotechnology

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    VânAnhNguyễn
    This document contains 5 questions about accessing and searching NCBI databases. [1] It searches the Taxonomy database for common names and sequence records of various species. [2] It uses the name "plague thrips" to search Nucleotide and finds its scientific name and sequenced genes. [3] A search of PubMed finds 2 publications by "Thanh NM" on striped catfish and giant freshwater prawn. [4] A search of the Genome database finds over 20 records for Homo sapiens and provides details on Chromosome 1. [5] Using the accession number "CU329670", it provides information on a sequenced chromosome of Schizosaccharomy

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    Bioinformatics Assignment 1: Accessing Ncbi Databases: International University - Vnu HCMC School of Biotechnology

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    VânAnhNguyễn
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    This document contains 5 questions about accessing and searching NCBI databases. [1] It searches the Taxonomy database for common names and sequence records of various species. [2] It uses the name "plague thrips" to search Nucleotide and finds its scientific name and sequenced genes. [3] A search of PubMed finds 2 publications by "Thanh NM" on striped catfish and giant freshwater prawn. [4] A search of the Genome database finds over 20 records for Homo sapiens and provides details on Chromosome 1. [5] Using the accession number "CU329670", it provides information on a sequenced chromosome of Schizosaccharomy

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    This document contains 5 questions about accessing and searching NCBI databases. [1] It searches the Taxonomy database for common names and sequence records of various species. [2] It uses the name "plague thrips" to search Nucleotide and finds its scientific name and sequenced genes. [3] A search of PubMed finds 2 publications by "Thanh NM" on striped catfish and giant freshwater prawn. [4] A search of the Genome database finds over 20 records for Homo sapiens and provides details on Chromosome 1. [5] Using the accession number "CU329670", it provides information on a sequenced chromosome of Schizosaccharomy

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    Download as docx, pdf, or txt
    83 views16 pages

    Bioinformatics Assignment 1: Accessing Ncbi Databases: International University - Vnu HCMC School of Biotechnology

    Uploaded by

    VânAnhNguyễn
    This document contains 5 questions about accessing and searching NCBI databases. [1] It searches the Taxonomy database for common names and sequence records of various species. [2] It uses the name "plague thrips" to search Nucleotide and finds its scientific name and sequenced genes. [3] A search of PubMed finds 2 publications by "Thanh NM" on striped catfish and giant freshwater prawn. [4] A search of the Genome database finds over 20 records for Homo sapiens and provides details on Chromosome 1. [5] Using the accession number "CU329670", it provides information on a sequenced chromosome of Schizosaccharomy

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    I.

    INTERNATIONAL UNIVERSITY – VNU HCMC


    II. SCHOOL OF BIOTECHNOLOGY
    III.

    BIOINFORMATICS

    Assignment 1:

    ACCESSING NCBI DATABASES

    Student name:

    Nguyễn Hà Vân Anh BTBTIU18004

    Văn Thị Ngọc Dung BTBTIU18047

    Nguyễn Ngọc Phương Uyên BTBTIU18269

    Trần Hoàng Phương Trinh BTBTIU18252

    Date of submission: Sat, Oct 17, 2020

    Contents

    Question 1: Search Taxonomy database.....................................................................................3

    Question 2: Use the name “plague thrips” to search the Nucleotide database...........................6

    Question 3: Search PubMed for “Thanh NM” (International University)................................12

    Question 4: Search Genome database for Homo sapiens.........................................................14

    Question 5: Use accession number “CU329670” to search the Nucleotide database...............16


    Question 1: Search Taxonomy database

    1) Homo sapiens

    2) Heterodoxus macropus,

    3) E.coli.

    a. What is the common name of the species?


    The common name for Homo sapiens is “human”.

    Figure 1.1A: Ìnformation for Homo sapiens from NCBI taxonomy database

    The common name for Heterodoxus macropus is “wallaby louse”


    .

    Figure 1.1B: Ìnformation for Heterodoxus macropus from NCBI taxonomy database
    Figure 1.1C: Results for “E.coli” from NCBI

    The common name for Escheria coli is E.Coli

    b. How many nucleotide or protein sequence records do you find (show your search
    results in cropped windows)?

    Figure 1.2A: Search results for nucleotide sequence in Homo sapiens

    There are 27,672,287 results for nucleotide sequence for Homo sapiens
    Figure 1.2B: Search results for protein sequence in Homo sapiens

    There are 1,423,829 results for protein sequence for Homo sapiens

    Figure 1.2C: Search results for nucleotide sequence in Heterodoxus macropus

    There are 2 results for nucleotide sequence and 26 results for protein in Heterodoxus
    macropus

    Figure 1.2D: Search results for nucleotide sequence in E.coli

    There are 8,458,194 results for nucleotide sequence in E.coli


    Figure 1.2E: Search results for protein sequence in E.coli

    There are 60,512,147 results for protein in E.coli

    Question 2: Use the name “plague thrips” to search the Nucleotide database.

    a. What is the scientific name of the plague thrips?

    Fig.2.1. Scientific name of plague thrips


    Choose 1 from the finding results, we have the scientific name of “plague thrips” is Thrips
    imaginis.
    b. How many sequence records do you find?
    Fig.2.2. Results sequences
    By using the key word “plague thrips” in nucleotide database, I found out 16 sequence
    records.
    c. Which genes or genomes of the plague thrips have been sequenced?
    - Mitochondrial genome:

    Fig.2.3. Sequenced Thrip imaginis mitochondrial genome


    - Elongation factor 1 alpha (EF1a) gene:
    Fig.2.4. Sequenced Thrip imaginis EF1a gene
    - Genes coding for 5.8S rRNA, ITS2 rRNA

    Fig.2.5. Sequenced Thrip imaginis 5.8S and ITS2 rRNA genes


    - 28S ribosomal RNA gene:

    Fig.2.6. Sequenced Thrip imaginis 28S ribosomal genes


    - 18S ribosomal RNA gene

    Fig.2.7. Sequenced Thrip imaginis 18S ribosomal genes


    - Histone 3 (H3) gene:

    Fig.2.8. Sequenced Thrip imaginis Histone 3 genes


    d. Provide information of the most recent publication that reported the
    mitochondrial genome of the plague thrips including the authors, year and title of
    the publication, title of the journal, volume, and page numbers.
    Thrips imaginis mitochondrion, complete genome – ID: AF335993.2
    Most recent
    publication

    Fig.2.9. Sequenced mitochondrial genome with publications


    - The most recent publication: Reference 2 ((bases 1 to 15407)
    o Authors: Shao,R. and Barker,S.C.
    o Title: The highly rearranged mitochondrial genome of the plague thrips, Thrips
    imaginis (Insecta: Thysanoptera): convergence of two novel gene boundaries
    and an extraordinary arrangement of rRNA genes
    o Year: 2003
    o Journal: Mol. Biol. Evol., vol 20, page: 362-370
    Question 3: Search PubMed for “Thanh NM” (International University).

    a. How many publications of Thanh NM were deposited in PubMed?

    There are 2 publications of Thanh NM were deposited in PubMed.

    b. List the common names of 2 aquatic animals that Thanh NM worked on.

    - Striped catfish (Pangasianodon hypophthalmus) 

    - Giant freshwater prawn (Macrobrachium rosenbergii)

    c. Provide information of publication by Thanh NM: year and title of the publication,
    title of the journal, volume and page numbers.

    - Publication 1:

     Title of the publication: A transcriptomic analysis of striped catfish (Pangasianodon


    hypophthalmus) in response to salinity adaptation: De novo assembly, gene annotation
    and marker discovery.
     Year: 2014
     Title of the journal: Comparative Biochemistry and Physiology. Part D, Genomics &
    Proteomics
     Page numbers: 52 – 63
     Volume: 10
    Figure 3.1: 1st publication by Thanh NM

    - Publication 2:

     Title of the publication: Optimizing de novo transcriptome assembly and extending


    genomic resources for striped catfish (Pangasianodon hypophthalmus).
     Year: 2015
     Title of the journal: Marine Genomics
     Page numbers: 87 – 97
     Volume: 23

    Figure 3.2: 2nd publication by Thanh NM


    - Publication 3:
     Title of the publication: A candidate gene association study for growth
    performance in an improved giant freshwater prawn (Macrobrachium
    rosenbergii ) culture line.

     Year: 2014

     Title of the journal: Marine Biotechnology (New York, N. Y.)

     Page numbers: 161 - 180

     Volume: 16

    Figure 3.3: 3rd publication by Thanh NM

    Question 4: Search Genome database for Homo sapiens.

    a. How many records did your search find?

    The search for Genome database for Homo sapiens illustrated 20 most recented records.
    Fig.1: Homo sapiens genome records

    b. Provide the GenBank accession number for the chromosome 1 of Homo sapiens, the
    size of the chromosome 1.

    _ The accession number of Chromosome 1 of Homo sapiens on GenBank: CM000663.2


    _ The size of chromosome 1: 248.96 Mb (248956422 bp)

    Fig.2: Chromosome 1 on Homo sapiens genome


    c. Provide information of the most recent publication that reported the chromosome 1
    including the authors, year and title of the publication, title of the journal, volume and
    page numbers.

    _ The most recent publication that reported the chromosome 1 is “The DNA sequence and
    biological annotation of human chromosome 1”
    AUTHORS Gregory, S., Barlow, K., McLay, K. et al.
    TITLE The DNA sequence and biological annotation of human chromosome 1
    JOURNAL Nature 441 (vol. 7091), page 315-321 (2006)

    Question 5: Use accession number “CU329670” to search the Nucleotide database.

    a. What is the type of sequence? What is the length of sequence? What is the name of
    database division?

    - Type of sequence: Chromosome I, complete sequence (DNA linear)

    - Length of sequence: 5579133 bp

    - Name of database division: Genbank database division

    Figure 5.1: Nucleotide database of ID “CU329670”

    b. What is the scientific name of organism?

    - The scientific name of organism: Schizosaccharomyces pombe.

    c. Name the protein product of the CDS and the length of protein.

    _ The name of protein product: RecQ type DNA helicase


    _ Length of the protein: 1887 aa
    Fig.3: Length of CDS product

    d. Write the first four amino acids.

    - The first four amino acids are Methyonine, Valine, Valine and Alanine

    Fig.4: Product of CDS and the first four amino acidsQuestion 5: Use accession number
    “CU329670” to search the Nucleotide database

    e. Write the nucleotide sequence of the coding strand that corresponds to these amino
    acids.

    The first four amino acids are Methionine, Valine, Valine and Alanine

    Amino acid Methionine Valine Valine Alanine

    Nucleotide ATG GTC GTC GCT


    sequence
    (coding)
    Nucleotide TAC CAG CAG CGA
    sequence (non-
    coding)

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