Practical - genetic databases
Practical time allocated: 1 hour
Activity 1: video
Use-of-a-database-to-determine-differences-in-the-base-sequence-of-a-gene-in-two-species.pdf Activity 1: Instructions
One outcome of the Human Genome Project is that the techniques that were developed have enabled the sequencing of other genomes. This allows gene sequences to be compared. The results of this comparison can be used to determine evolutionary relationships. Also, the identification of conserved sequences allows species to be chosen for exploring the function of that sequence.
Go to the Gen Bank linked to below
Choose ‘gene’ from the search menu
Enter the name of a gene plus the organism, such as cytochrome oxidase 1 (COX1) for pan (Chimpanzee)
Under the ‘Genomic regions, transcripts and products’ click ‘go to nucleotide: FASTA’
Copy the sequence that appears and paste it into a text file by using the following steps on a mac:
a. Open textedit
b. Click “new document”
c. Under format click “make plain text” d. Paste your sequence
You can paste multiple sequences in the same text file (note: if you delete the numbers at the top but keep the >gi| followed by the name of the organism whose sequence you have this will make the final steps easier.
Repeat for five species of your choice (include at least one plant and one bacteria in your search and save the file with a suitable name)
Download the software ClustalX 2.1
Add the application to your applications folder
Run the application
In the File menu choose ‘load sequences’
Select your file. Your sequences should appear in the Clustal X window.
Under the alignment menu choose ‘Do complete alignment’.
The output files can be analysed in another program to produce phylogenetic trees (DP Topic 5.4)
Activity 2: Video
Use-of-a-database-to-determine-differences-in-the-base-sequence-of-a-gene-in-two-species.pdfActivity 2: instructions
This practical has been adapted from Inthinking.co.uk and Allott & Mindorff 2014. You will use the Ensembl database to complete the table opposite
Search for Ensembl Genomes
Use the tabs in the top right to Navigate between Vertebrates (H. sapiens,
P.Troglodytes, C. familiaris), Metazoa (D. melanogaster), Bacteria (E.coli) and Plants (O. sativa).
In each tab search for the species in question under ‘browse genome’.
When the species if selected click ‘view karyotype’
Count the number of chromosomes in the karyotype image to find the diploid number.
The number of base pairs will give you the Genome size
The number of coding genes will give you the number of genes
Activity 3: Video
Use-of-a-database-to-determine-differences-in-the-base-sequence-of-a-gene-in-two-species.pdfActivity 3: Instructions
The locus of a gene is its particular position on the homologous chromosomes. Online databases can be used to find the locus of human genes. There is an example of such a database in the Online Mendelian Inheritance in Man website, maintained by John Hopkins University.
Google the abbreviation OMIM to open the homepage
Choose search ‘Gene Map’ in the Advanced Search settings
Enter the name of a gene into the Search Gene Map box. This will bring up a table
with information about the gene including its locus.
Complete the table below.
