Amazing Science Facts

Different methods of gene sequencing

This blog will cover the different types of sequencing methods that you can use to learn about your genes and how they are used in gene expression studies. I will also show you ways to do this with your cells!

Before we get into each method, let’s understand what exactly a gene is. A gene is any site on the bacterial chromosome that is involved in the growth of bacteria. Each gene has only one site on it and is also called a locus. A locus determines where the DNA sequence begins and ends.

Now let’s look at what we mean by “sequence”. When a person reads their paper or book, they read all the words on it and not just the ones on your paper! We have to read our entire textbook before the chapter on biology (e.g., The Biology course or AP Biology course) or watch the videos for lessons 1-5 and then move on to study the video materials you watched. To be sure we need to figure out what each word means so as not to miss anything important. Also, we need to know which part of the chapter does which section of information depending on our topic and your learning level. We do not just jump into your chapters or videos without first understanding how they work. When we go to college, for example, we get taught several topics like physics, chemistry, etc. So when we talk a certain way we get an idea of how these topics work. If we say someone wants to study mathematics, for example, we don’t just start from nothing. Instead, we first get our foundations for mathematical equations and then apply them to real-life problems. Why is it that we are only able to learn math because of the number of people who thought it was important? Because they understood the concepts and how to use them. It took lots of practice and effort before you could think logically and apply it to everyday situations. Same concept for science and why it takes years to master something like a language. You do not just read books in that language and apply your knowledge everywhere. That is done by time and dedication and hard work. There is no point jumping directly into the material you want to write that you found online. People are busy making money and they prefer to sit down with a pencil and paper. Yes, you can make a mistake but most likely it is an error. Just try again.

Now, there are many different kinds of biological samples you can take. For instance, from a patient, you can take blood samples from cancer patients. Then you want to be careful since these samples are very sensitive so they cannot be analyzed very often. From a mouse, you can take the tissue from its brain. Next, from humans, you may take all the blood in their whole body like arm, leg, brain, etc. All of these samples are collected from animals so you need to make sure that the animal is healthy before collecting samples from it. Another sample that might be taken is from the soil, air, water, etc. These samples are also sensitive so you need to thoroughly analyze the samples you are given. How did the virus affect those humans or mice? Was it poisonous or any other harmful thing? Did the treatment of the human or mouse work or not? What diseases affected the mice or humans? Was the treatment effective? Are they still alive, if so what kind? They can contain viruses but only in small amounts. Usually, scientists only run such analyses once per year or less. So in case, you were studying genetic effects on animals, humans, or another virus that might kill us, then you need to do it several times to be sure the sample was not contaminated or contaminated and be sure it is free from the harmful effect of the virus. If you find out you are infected with the virus, then you have to isolate it from the environment and then test. After isolating it you have to do tests to see if the treatment worked or not. And after checking all the results and data, you need to draw conclusions and decide which one is accurate and correct. Is it the right treatment for the disease or gene affected?

There are two types of analysis performed on a given sample. One is looking for mutations and the other is finding the gene that does what the patient needs. The mutation is the change of one nucleotide to another. When you change one base to another in the genome that is called a mutation. Sometimes it happens due to errors during cell division or sometimes due to the random fluctuation of the environment. Mutations are mostly done by mistakes during cell division or other reasons too. By observing a few such examples, and comparing them to our previous knowledge we can figure out what kind of mistakes and causes they occur. On the other hand, finding the gene that does what the patient needs also known as the functional gene is called the marker gene as in the name. As we know, the same RNA (genome) that acts as a template for gene transcription is called the marker gene and it tells us which gene is being transcribed. Therefore, finding the gene that does what it does in humans or mice is called mapping the genome of the organism. With the help of molecular tools such as cDNA techniques, we can tell where it sits, whether it is translated in the original form or if it has mutated.

Different approaches can be used to do these analyses. Several are l techniques are used to identify the functional genes of SARS-CoV-2 genomes. One approach was to find the open reading frames (ORF) in the mRNA for the spike protein. ORFs can play a major role in cell signaling in the form of transcriptional regulation. By analyzing a large database of protein sequences, the ORF-based approach allows us to discover new functional proteins that are essential for coronavirus replication. An interesting fact that scientists discovered in the process were that some of the genes of coronavirus encode a non-structured nucleoprotein (NSP). Research indicates that NSPs are the primary targets for viral entry in cells (the envelope protein can bind to specific receptors on the host cell surface). Using this approach to analyze this protein we can see if the NSPs of the spike protein mutated because it is associated with cell entry and/or infection.

Another technique to screen for mutation is through the search for potential homologous in the target protein sequence. Homologs refer to the sequences that exhibit similarities between the protein, including amino acid sequences. During the identification of the functional protein from the SARS-CoV-2 spike protein, scientists developed a computational algorithm to explore how many pairs of amino acids with high probability correspond to matches between sequences. In principle, this approach allowed scientists to scan thousands of sequences and locate the appropriate functional homologs for the spike protein. This approach was named Proportion Prediction.

The other method that uses a similar approach is to select an optimal structure for the target protein by scanning the database for possible structures. The goal of this approach was to find out which structure would maximize protein efficiency. Scientists have made progress in using artificial intelligence to develop models of how the ribosomes will bind to and cleave the target proteins. Once the model was designed, an in vitro system could be built to create a model of the target protein and its binding to the ribosomes. 

Next, two independent groups conducted experiments to demonstrate the effectiveness of both approaches. They combined two approaches with similar proteins to determine how well the structural data from either approach could be linked together, they split the data into two groups and ran separate experiments to compare the experimental values obtained from the two approaches. Both approaches resulted in identical functional predictions, but the second approach generated many more false positives. The researchers concluded that because the second approach generates multiple copies of each set of amino acids, it will have produced significantly fewer positive predictions. Although the second approach may produce a higher proportion of true positive predictions, it must be noted that the actual impact a particular mutation had at the cellular level should be considered. Hence, I think this is another good reason why it is extremely useful to conduct experiments and analyze your data. Maybe you need to know which parts to cut out; which regions to edit; how important each region delete or add; why you would remove this or put this or which part of that particular mutation should be deleted. Here in this blog post, I will only explain the steps and describe how the code works in detail. Let me know if you have questions or ideas. I am always happy to help.