Visualising DNA, RNA & Proteins Jalview School Workbook Resources

Visualising DNA, RNA and proteins workbook is aimed at 16-18 year old secondary school students studying Higher, Advanced Higher or A level biology.
The easy-to-use design requires only a desktop or laptop computer with a web browser and internet access.
The workbook contains 4 practical web-based bioinformatic projects:
  Project 1 views DNA and RNA sequences and their 3D structures.
  Project 2 views protein sequences and their 3D structures.
  Project 3 compares the sequence of human myoglobin protein with myoglobin sequences from other animals; then the student views the coding DNA sequence, and codons, alongside the protein.
  Project 4 views exons and introns in the human haemoglobin subunit beta (HBB) gene. This is the gene involved in sickle cell anaemia, an inherited red blood cell disorders which affects millions of people throughout the world. The genetic mutations linked to this disease is identified by viewing the coding DNA and its protein product in a split-screen viewer.

Getting started:
(i) Click on the ‘View the School Workbook’ link in Section 1 to open the booklet in an adjacent window, or download the pdf depending on the browser.
(ii) Follow the instructions in the workbook, the links in Section 2 start each exercise by launching JalviewJS and loading the sequences.
If you get stuck, the videos in section (b) may help.

(1) Click to View the School Workbook in an adjacent web browser tab.

(2) Follow the Instructions in the School Workbook

Use the links below to open JalviewJS in the web browser and view the molecules.
Note it may take a few seconds to open JalviewJS and load the sequences.

Project 1-Exercise 1: Click to  View DNA fragment (3BSE) in JalviewJS
Project 1-Exercise 2: Click to  View RNA (2GIS) in JalviewJS
Project 2-Exercise 1: Click to  View Myoglobin protein (1mbn - transport) in JalviewJS
Project 2-Exercise 1: Click to  View Collagen protein (1cag - structure) in JalviewJS
Project 2-Exercise 1: Click to  View Amylase protein (1smd - enzyme) in JalviewJS
Project 2-Exercise 1: Click to  View Antibody protein (1igt - storage) in JalviewJS
Project 2-Exercise 1: Click to  View Insulin protein (6bcx - signalling) in JalviewJS
Project 2-Exercise 1: Click to  View Ferritin protein (5xb1 - storage) in JalviewJS
Project 3-Exercise 1: Click to View Myoglobin Sequences and create a Tree in JalviewJS
Project 3-Exercise 2: Click to View Myoglobin protein & its coding DNA in JalviewJS by reading in file CAG46747 from EMBLCDS database
Project 4-Exercise 1: Click to View Exons & Introns in the HBB gene in JalviewJS
Project 4-Exercise 2: Click to View the coding DNA & its protein product in JalviewJS by reading in file CAG46711 from EMBLCDS database

(a) What is Jalview?

Jalview is one of the most widely used applications for visualising and analysing DNA, RNA and protein multiple sequence alignments. It is free-to-use computer software with an interactive multi-window interface. This allows researchers to read files directly from public biological databases and view sequences, 3D structures and evolutionary trees. Jalview has a number of analysis tools for aligning sequences, measuring similarities, exploring features and comparing structures. Jalview has been developed in Prof Geoff Barton's group in School of Life Sciences the University of Dundee, with the funding support of the BBSRC and the Wellcome Trust.

(b) Getting Started, Walkthrough, Help Videos

 

 

Click to view the Getting Started using Jalview videos.
Click to view all the Jalview training videos.
These videos are located on the Jalview Online Training YouTube channel.

(c) Database Identifiers and Links

PDB IDs used in Project 1 & 2

PDB ID Molecule Function Link
3DSE DNA fragment  

http://pdb101.rcsb.org/motm/23

2GIS RNA  

http://pdb101.rcsb.org/motm/15

1smd Amylase Enzyme

http://pdb101.rcsb.org/motm/74

1cag Collagen Structure

http://pdb101.rcsb.org/motm/4

1igt Antibody Defence

http://pdb101.rcsb.org/motm/21

5xb1 Ferritin Storage

http://pdb101.rcsb.org/motm/35

6bcx Insulin Signalling

http://pdb101.rcsb.org/motm/14

1mbn Myoglobin Transport

http://pdb101.rcsb.org/motm/1

Uniprot Myoglobin IDs used in Project 3

Uniprot ID

Species

P02144 Human
P02147 Gorilla
P02185 Whale
P02192 Cow
P04247 Mouse
P68276 Dolphin
P02197 Chicken
P63113 Dog
P02190 Sheep
P02187 Elephant

P02144; P02147; P02185; P02192; P04247; P68276; P02197; P85077; P63113; P02190; P02187

DNA Identifier Codes used in project 3 & 4

CAG46747 EmblCDS ID for MB gene that codes for myoglobin protein (P02144)
CAG46711 EmblCDS ID for HBB gene that codes for Hemoglobin subunit beta protein (P68871)

Free Public Biological Databases

(i) UniProt is a database of protein sequences (http://www.uniprot.org/).
(ii) Protein Data Bank (PDB) is a database of crystallographic, three-dimensional structural data of large biological molecules (http://www.rcsb.org/).
(iii) Ensembl is a genomic database (http://ensemblgenomes.org/).
(iv) EMBL (CDS) data originates from the European Nucleotide Archive (ENA) database of annotated DNA and RNA sequences (https://www.ebi.ac.uk/ena).
(v) PFAM is a database of protein families is a database of protein families (http://pfam.xfam.org/)
(vi) RFAM is a database containing information about non-coding RNA families and other structured RNA elements (https://rfam.xfam.org/).

(d) Acknowledgements

The workbook was produced by Suzanne Duce with help from Mungo Carstairs, Benedict Soares, Bob Hanson, Dmitry Finkelbergs, Charlotte Campbell, Jim Procter and Geoff Barton.

(e) Other Links

Blackboard Collaborate Workshop Instructions

 

Project 1 feedback form

https://docs.google.com/forms/d/e/1FAIpQLScjwWzA6FKdvJ19zhyoBM1YE6W2CQfzczijVfnp__-65WWk4Q/viewform

 

Project 2 feedback form

https://docs.google.com/forms/d/e/1FAIpQLSdDcRXmRXkg9YcxPiY_kTLoexDJyt3N5KJHIC5OXSA07L5uSw/viewform

 

Project 3 feedback form

https://docs.google.com/forms/d/e/1FAIpQLSer8cBMkMfHIZntnfesuszx-iKm3GtojyXkxycrIq1GzTzEww/viewform

 

Project 4 feedback form

https://docs.google.com/forms/d/e/1FAIpQLSfZc3KIuoL4liwL-dzTBCQ8dhT6T5-gkgxcEOSY2yvBGIQIJA/viewform

 

Low resolution version of the School Workbook