Scribd
Upload
16 views

Bioinformatics Practical Assignment (1)

The document provides an introduction to bioinformatics and functional genomics, focusing on three key tools: Reverse Complement, AmplifX, and BLAST. It explains the importance of reverse complement sequences in molecular biology, details the process of designing PCR primers using AmplifX software, and describes how to use BLAST for comparing biological sequences against known databases. Overall, it serves as a guide for utilizing these tools in molecular biology research.

Uploaded by

sohailsaleem8456
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
16 views

Bioinformatics Practical Assignment (1)

The document provides an introduction to bioinformatics and functional genomics, focusing on three key tools: Reverse Complement, AmplifX, and BLAST. It explains the importance of reverse complement sequences in molecular biology, details the process of designing PCR primers using AmplifX software, and describes how to use BLAST for comparing biological sequences against known databases. Overall, it serves as a guide for utilizing these tools in molecular biology research.

Uploaded by

sohailsaleem8456
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 25

Introduction to Bioinformatics

and Functional Genomics

Submitted by: M.Sohail Saleem


Registration: 2023-uam-5858
Submitted to: Dr. Shoaib
Contents
• Reverse compliment
• AmplifX
• BLAST
Reverse Compliment
In molecular biology, the reverse complement of a DNA or RNA sequence is a sequence
that runs in the opposite direction (reverse) and has complementary base pairs. This is
crucial for understanding the structure and function of nucleic acids. In Polymerase
Chain Reaction (PCR), primers are designed to be complementary to the target DNA
sequence. One primer is a forward primer, and the other is a reverse primer, which is the
reverse complement of the forward primer. Reverse complement is used in various
molecular biology techniques, such as DNA sequencing, Southern blotting, and Northern
blotting.
Following procedure can be used to effectively generate and analyze reverse
complementary sequences.
Look up for Reverse-Complement.com using Chrome or
Edge, then proceed to access its interface
The Reverse-Complement interface features an empty box for
pasting your FASTA sequence, followed by clicking the
submit option.
Once you submit, you will receive the reverse complementary
sequence required.
AmplifX
AmplifX is a free software designed for primer design, management, and testing. It's a
valuable tool for molecular biologists and researchers involved in polymerase chain
reaction (PCR) experiments.
AmplifX allows you to design primers for specific DNA sequences based on various
parameters, including: Primer length
• Melting temperature (Tm)
• GC content
• Self-complementarity
• Hairpin formation
First of all, we open AmpliX Software and we get some options
displayed on the screen, with a blank box.
After that, we go to the 'File' option and click on 'Open' to target the
sequence.
After clicking on the 'Target Sequence' option, we navigate to our PC
to select a file, and then we select the sequence that we had obtained
from NCBI earlier.
Then we select the sequence and it gets pasted into AmplifX.
After that, we need to select the 'Primers' option and click on
“Design Primers”.
After that, we will be asked about some things such as Primer Length,
TM Difference, GC Clamp, and Number of Best Primer Pairs etc.
If you want, you can make changes according to your preferences or
leave it as default and then click on the Find button at the corner.
A few seconds later, we will get the sequence for the forward and
reverse primer pairs.
After that, select one of the pairs and click on the Add to Primer list button.
length, quality, and TM, as well as some other details.
After

And then you will see the details of the primer's length, quality, and TM, as well
as some other details. After that, click on the Run PCR button at the corner, and
your PCR run will be completed.
When you click on the purple line below the sequence, you will see the full details
of the sequence, including the number of nucleotides (bp) that make up the
forward primer and reverse primer, and where they are attached.
BLAST
BLAST stands for Basic Local Alignment Search Tool. It's a computer program that is
widely used in bioinformatics to compare biological sequences (DNA, RNA, or protein)
against databases of known sequences.
1. Input sequence: You provide the sequence you want to search with.
2. Database: You specify a database of known sequences to compare against.
3. Alignment: BLAST searches for regions of similarity between your input sequence
and the sequences in the database. These regions are called "hits."
4. Scoring: The hits are scored based on the degree of similarity and the statistical
significance of the match.
5. Results: BLAST returns a list of hits, ranked by their score, along with information
about the matching sequences, such as their species, gene name, and function.
Launch Edge or Chrome and look up NCBI. Once you find it, navigate to
NCBI's interface. You'll find options on the right side, including one for
Blast. Select Blast to access the Blast interface.
Further down the page, there are choices for comparing Nucleotide to
Protein and Protein to Nucleotide.
"Convert Nucleotide to Protein" or "Convert Protein to Nucleotide." After choosing, a new tab or page will
open, providing the option to input either a Query Sequence or FASTA Sequence. In this area, you can paste
your sequence, whether it is a nucleotide or protein sequence, based on the conversion you require.
Once you have pasted your sequence, you can scroll down the page to find the BLAST
button located on the left side. Simply click on the BLAST button to start the sequence
analysis or conversion process.
After clicking on the BLAST button, your sequence will be processed, and a detailed report will appear shortly after.
This report will provide extensive information about your sequence, including alignments, matches, and other pertinent
data. You can then examine these results to obtain a complete understanding of your sequence analysis or conversion.
Upon examining the comprehensive report, continue scrolling, and you'll
come across a list of sequences that closely resemble your input sequence.
SUMMARY
We learned:
• To design PCR primers using AmplifX Software
• Use of BLAST to compare biological sequences (DNA, RNA, or protein) against
databases of known sequences.
• Use of tools and techniques to generate Reverse Complement Sequences

You might also like