Introduction to Bioinformatics online course: IBT
Practical Assignment
Module name: Introduction to Databases and Resources
Session name: Bioinformatics Databases and Resources
Trainer: Shaun Aron
Participant: <write your name here>
Date: <write today’s date here>
Bioinformatics Databases
Introduction
Please go through the entire practical exercise. No formal answers are required for
Task 1 and Task 2. These two sections of the practical are focused on you exploring
and becoming familiar with the two resources. You are welcome to make your own
notes and comments for these two sections. Please complete the answers for Task3:
Finding and extracting information section ONLY in this document and upload this
to the Vula website before the deadline for submissions.
Tools used in this session
NCBI www.ncbi.nlm.nih.gov
EBI www.ebi.ac.uk
Please note
Hand-in information If you are formally enrolled in the IBT course, please upload
your completed assignment to the Vula ‘Assignments’ tab. Take note of the final
hand-in date for each assignment, which will be indicated on Vula.
Task 1: Exploring the NCBI resources
Task 1: Instructions
Open a browser and navigate to the main NCBI webpage (www.ncbi.nlm.nih.gov):
1. Describe briefly what resources are found in each section of the webpage:
a. The left hand panel
b. The right hand panel
c. The centre panel
Introduction to Bioinformatics online course: IBT
d. The lower panel
2. From the right hand panel or the drop down menu (select the database and
leave the search box empty and click search to access a database or resource
homepage) navigate to the homepage for the following resources and
describe what each resource is used for:
a. PubMed Central
b. Genome
c. PubChem
d. SRA
e. dbGap
3. Navigate to the Gene resource and have a look at the types of queries that
can be used to search for information. (No answer necessary)
4. Select the DNA and RNA tab from the menu on the left on the homepage.
a. What information does the RefSeqGene database contain?
b. What are the download and submission tabs used for?
Task 2: Exploring the EBI resources
Task 2: Instructions
Open another browser window and navigate to the EMBL-EBI webpage
(www.ebi.ac.uk):
1. Navigate to the services page.
a. How are the resources/databases categorised in comparison to NCBI?
b. Select the DNA and RNA category. Compare the resources and
databases available here in comparison to NCBI. Briefly describe what
the main differences are.
2. Navigate to the Uniprot website from the homepage.
a. What is the resource used for?
Task 3: Finding and extracting information
Task 3: Instructions
1. You are about to conduct a study examining the genetic variation present in
the LDLR gene in a local population group in your country. As a starting point
you would like to find all relevant information on the gene. Using either the
NCBI or EBI resources, find the following information about the gene.
a. What is the full name of the gene?
b. What is the chromosome number and genomic location of the gene?
Introduction to Bioinformatics online course: IBT
c. How many protein-coding transcripts have been annotated for the
gene?
d. Provide a brief description of the function of the protein encoded by
the LDLR gene.
e. What is the accession number for the genomic sequence for the
GenBank entry for the gene?
f. Is there a RefSeq entry for the LDLR gene? If so, provide the accession
number of the sequence from which the RefSeq was derived.
g. What disease is associated with mutations in the LDLR gene? Provide
the associated OMIM entry number for the disease.
h. Provide a citation (in any format) for a journal article that identified
variants in the LDLR gene linked to hypercholesterolemia.
i. What is the accession number for the longest RefSeq mRNA and
protein sequence encoded by the LDLR gene?
j. What is the length of the protein encoded by the longest LDLR
transcript?
k. Extract and paste the amino acid sequence for the longest protein
encoded by the LDLR gene.
Task 3: participant’s answer
<start typing your answer here>
