+:+Assignment 1+:+

How to use Bioinfomatics tool from www.in-silico.com to perform PCR amplification

1. This is online-tool so first step that you have to do is open this web site by insert http://www.in-silico.com in address box on your internet explorer. Then you will see this picture on your screen.

This web site allow you to perform in silico experiments with complete genomes both prokariotic and eukariotic genomes.
The example of experiments

PCR amplification
Multiplex PCR
Restriction digest and PFGE
PCR-RFLP
Double Digestion fingerprinting
AFLP-PCR
SRF fingerprinting
Find ORF by name
Sort sequence locator

Beside in silico experiments, this site have other tools such as

DNA restriction digest
Compare restriction patterns of two sequences for SNP/Mutation detection
Restriction enzymes: vendors
Translate DNA to protein
Colored sequences for presentations
Basic Tm calculation

In this assignment, I will show only in silico experiment by performing PCR with complete genome of Mycobacterium tuberculosis so click on “PCR amplification” icon.

2.Then you will see this picture on your screen.

This page show you the list of organism’s complete genomes.In my sample, click on “Mycobacteria”.

3.Put sequence of your Primers, select Mycobacteria species and set Maximum lenght of PCR product as shown in this picture.Then click “Amplify”

4.The result of PCR will be show in this page.You will get the position and size of PCR product.Then click on Position of amplification to see your PCR product sequence.

5.This page shows PCR product sequence, start and end position of PCR, links to other tools such as tools for translate to protein, Restriction digest, BLAST, design primers and Map on NCBI.

6.use other tools perform experiments with your PCR product.

Translate sequence to protein, you will get result as shown in this picture.