BIOINFORMATICS

WORKSHEET

1.Choose a inherited disorder, select a pathway for this disorder. Extract
transcripts, UTR sequences using Ensemble biomart.

2. Choose one protein coding transcript from the respective gene. Design primers
from two exons (Note: There should be intron between two exons). Verify using
an in-silico PCR showing only exonic amplification. Try to do primer designing
manually.

3.Identify a SNP of the gene from the exonic sequence selected for amplification.

4. Extract sequence of a mammalian expression vector pcDNA3.1

5. Clone your amplified sequence in the plasmid by adding restriction sites in
your designed primer. You can use Ape program for this purpose. The cloned
sequence should be highlighted.

6. Modify your primer so that you can mutagenize the normal sequence to the
SNP.

7. Identify microsatellite of the selected gene.

8. Find Alu repeats in the 3UTR of the transcript with complete information of
their orientation, repeat start and stop site.

9. Enlist your genes on gene ontology basis using any web based program do not
do it manually.

10. Give the gene expression data of your gene in relation to the disease/organ.

11.Perform a blast search of the gene. Retrieve similar gene sequences (highly
similar, moderately similar and less similar). 3 from each category. Perform
multiple sequence alignment and make a phylogenetic tree.

12. Find microRNA binding site in your selected transcript 3UTR.