Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
Scribd
Upload
152 views

Assignment 1 - Database - Oct 2021

This document provides instructions for an assignment on accessing and using NCBI databases. It includes 5 questions asking students to search various databases like Taxonomy, Nucleotide, PubMed, Genome, and access specific sequences to answer questions about species names, gene sequences, publications, and more. Key details to report include scientific names, accession numbers, sequence lengths, protein names and sequences, and publication authors and titles.

Uploaded by

Hồ Nguyễn Minh Thư
Copyright
© © All Rights Reserved
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
152 views

Assignment 1 - Database - Oct 2021

This document provides instructions for an assignment on accessing and using NCBI databases. It includes 5 questions asking students to search various databases like Taxonomy, Nucleotide, PubMed, Genome, and access specific sequences to answer questions about species names, gene sequences, publications, and more. Key details to report include scientific names, accession numbers, sequence lengths, protein names and sequences, and publication authors and titles.

Uploaded by

Hồ Nguyễn Minh Thư
Copyright
© © All Rights Reserved
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
You are on page 1/ 5

BT203IU Bioinformatics

Assignment 1

Accessing NCBI databases

Due date: 19:00 Mon. 4 Oct. 2021

(Submission via email: Bioinfosiu@gmail.com)

Aim of assignment 1

Learn how to access and use NCBI databases

Question 1: Search Taxonomy database for: 1) Homo sapiens, 2) Heterodoxus macropus, 3)


a. What is the common name of the species?
1) Human 2) wallaby louse 3) E. coli

b. How many nucleotide or protein sequence records do you find (show your search results in
cropped windows)?
Question 2: Use the name “plague thrips” to search the Nucleotide database.

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


Thrips imaginis
b. How many sequence records do you find? 16
c. Which genes or genomes of the plague thrips have been sequenced?
 Mitochondrial genome, EF1, COI genes and genes for 5.8S rRNA, ITS2, 28S rRNA

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.
Author: Nguyen,D.T., Spooner-Hart,R.N. and Riegler,M.

Year: 2015

Title: Polyploidy versus endosymbionts in obligately thelytokous thrips

Journal: BMC Evolutionary Biology 15 (1), 23 (2015)

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

a. How many publications of Thanh NM were deposited in PubMed? 5


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.
1. Thanh NM, Luyen ND, Thanh Tam Toan T, Hai Phong N, Van Hop N. Voltammetry
Determination of Pb(II), Cd(II), and Zn(II) at Bismuth Film Electrode Combined with 8-
Hydroxyquinoline as a Complexing Agent. J Anal Methods Chem. 2019;2019:4593135.
Published 2019 Jul 3.
2. Hoang VM, Le TV, Chu TTQ, et al. Prevalence of autism spectrum disorders and their
relation to selected socio-demographic factors among children aged 18-30 months in
northern Vietnam, 2017. Int J Ment Health Syst. 2019;13:29. Published 2019 Apr 29.
3. Thanh NM, Jung H, Lyons RE, et al. Optimizing de novo transcriptome assembly and
extending genomic resources for striped catfish (Pangasianodon hypophthalmus). Mar
Genomics. 2015;23:87-97.
4. Jung H, Lyons RE, Li Y, et al. A candidate gene association study for growth performance
in an improved giant freshwater prawn (Macrobrachium rosenbergii ) culture line. Mar
Biotechnol (NY). 2014;16(2):161-180.
5. Thanh NM, Jung H, Lyons RE, et al. A transcriptomic analysis of striped catfish
(Pangasianodon hypophthalmus) in response to salinity adaptation: De novo assembly, gene
annotation and marker discovery. Comp Biochem Physiol Part D Genomics Proteomics.
2014;10:52-63.
1/ Voltammetry Determination of Pb(II), Cd(II), and Zn(II) at Bismuth Film Electrode Combined
with 8-Hydroxyquinoline as a Complexing Agent (2019) - Journal of Analytical Methods in
Chemistry – Volume 2019 – 11 pages
2/ Prevalence of autism spectrum disorders and their relation to selected socio-demographic
factors among children aged 18–30 months in northern Vietnam, 2017 (2019) - International
Journal of Mental Health Systems – 9 pages 
3/ Optimizing de novo transcriptome assembly and extending genomic resources for striped
catfish (Pangasianodon hypophthalmus)  (2015) – Marine Genomics – 11 pages
4/ A Candidate Gene Association Study for Growth Performance in an Improved Giant
Freshwater Prawn (Macrobrachium rosenbergii) Culture Line (2013) -  Springer
Science+Business Media New York - Volume 2013 – 20 pages (161 – 180) 
5/ A transcriptomic analysis of striped catfish (Pangasianodon hypophthalmus) in response to
salinity adaptation: De novo assembly, gene annotation and marker discovery (2014) -
Comparative Biochemistry and Physiology, Part D – 12 pages ( 52 – 63) 

Question 4: Search Genome database for Homo sapiens.

a. How many records of genome assemblies did your search find? 1020
b. Provide the GenBank accession number for the chromosome 1 of Homo sapiens, the size of
the chromosome 1. “CM000663 & 248956422 bp”

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.

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


a. What is the type of sequence? (DNA) What is the length of sequence? (5579133 bp) What is the
name of database division? PLN (Plant, fungal, and algal sequences)
b. What is the scientific name of organism? (Schizosaccharomyces pombe)
Go to the FEATURES section of the record. Link to the CDS to gain access to the first 5662
nucleotides of the sequence.
c. Name the protein product of the CDS and the length of protein.
RecQ type DNA helicase. It contains 1887 amino acids
d. Write the first four amino acids.
Methionine M ,Valine V,Valine V, Alanine A.
e. Write the nucleotide sequence of the coding strand that corresponds to these amino acids.
5'ATGGTCGTCGCT3'
f. Write the nucleotide sequence of the template strand that corresponds to these amino acids. (Note
that the definition of the coding strand is the strand of DNA within the gene that is identical to
the transcript and the template strand is the strand that is complementary to the coding strand.)
3'TACCAGCAGCGA5' template strand

You might also like