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Resources for the Jalview Schools Workbook

'Visualising DNA, RNA & Proteins' Jalview Schools Workbook is aimed at 16-18 year old secondary school students studying 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 3 practical web-based projects:
Project 1 views DNA, RNA and protein sequences, then views the 3D structure of these molecules.
Project 2 views the sequence and structure of human myoglobin protein, comparing it with myoglobin sequences from other species. The student then views the coding DNA sequence, and codons, alongside the protein.
Project 3 views exons and introns in the HBB gene (which is involved in sickle cell anaemia). The student then views the coding DNA and its protein product in a split-screen viewer identifying the genetic mutations linked to the disease.

(A) School Workbook

Click here to view the School Workbook

(B) Launching Jalview JS program in a web browser

Click this link to launch JalviewJS

(C) IDs and URLs used in the Workbook

(a) Project 1-Exercise 1 ID: Viewing DNA (3BSE) - drag this DNA file onto Jalview desktop

(b) Project 1-Exercise 2 ID: Viewing RNA (2GIS) - drag this RNA file onto Jalview desktop

(c) Project 1-Exercise 3 IDs: Viewing protein Amylase (1smd enzyme) - drag this amylase file onto Jalview desktop

Collagen (1cag structure) - drag this collagen file onto Jalview desktop
Antibody (1igt defence) - drag this antibody file onto Jalview desktop
Ferritin (5xb1 storage) - drag this ferritin file onto Jalview desktop
Insulin (6bcx signalling) - drag this insulin file onto Jalview desktop [Note: this can take a while to load]
Myoglobin (1mbn transport) - drag this myoglobin file onto Jalview desktop

(d) Project 2-Exercise 1 ID: Viewing myoglobin sequences

Drag Myoglobin-p02144 file URL onto Jalview desktop
Drag Alignment of Myoglobins file URL onto Jalview desktop

(e) Project 2-Exercise 2 ID: Viewing myoglobin & its coding DNA - EMBLCDS database id: CAG46747

(f) Project 3-Exercise 1: Viewing exons & introns in the HBB gene

Drag HBB gene file URL onto Jalview desktop
Drag HBB feature file URL onto Jalview desktop

(g) Project 3-Exercise 2: Viewing coding DNA & its protein product - EMBLCDS database id: CAG46711

Drag HBB CDS feature file URL onto Jalview desktop
Drag Protein feature file URL onto Jalview desktop

Getting Started Video

Getting started can be achieved in 3 simple steps as demonstrated in the '1-minute set-up' video below.
(1) Open the school resources webpage on the Jalview website (https://www.jalview.org/school-resources)
(2) View the workbook pdf in a second window by clicking a link on the webpage
(3) Launch JalviewJS from a link on the webpage

Walkthrough Videos

The video walkthroughs are speeded up recordings of each of the exercises in the workbook.
(a) Click to view: Project 1-Exercise 1: Viewing DNA walkthrough video
(b) Click to view: Project 1-Exercise 2: Viewing RNA walkthrough video
(c) Click to view: Project 1-Exercise 3: Viewing proteins walkthrough video
(d) Click to view: Project 2-Exercise 1: Viewing myoglobin protein walkthrough video
(e) Click to view: Project 2-Exercise 2: Viewing myoglobin and coding DNA walkthrough video
(f) Click to view: Project 3-Exercise 1: Viewing exons and introns walkthrough video
(g) Click to view: Project 3-Exercise 2: Viewing coding DNA and its protein product walkthrough video

Other Videos

(i) What is Jalview?

 

(ii) Jalview- free software for multiple sequence alignment and analysis

 

(iii) Navigating the Jalview desktop


(iv) Click to view the video: Jalview's multiple windows

(v) Click to view the video: Jalview's drop-down and context menus

 

Identifier Codes used in the Workbook

Project 1 PDB IDs

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

Project 2 Uniprot Myoglobin IDs

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

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/).