Marker Genes and Gene Prediction of Bacteria

Posted on by Vijini Mallawaarachchi

When we think of the word marker, the first thing that comes to our minds is something that is used to indicate a place. For example, it can be your current location on Google Maps or it can be the place where you planted some seeds in your garden. Similarly, in genomics studies, we can find marker genes in bacterial genomes. In this article, I will introduce you to marker genes used in metagenomics analysis, how they are used and walk you through an example of a commonly used gene prediction tool.

Continue reading Marker Genes and Gene Prediction of Bacteria

Assessing the Quality of Genome Assemblies using QUAST

Posted on by Vijini Mallawaarachchi

The assembly algorithms that have been developed so far intend to provide better assemblies evaluated under different criteria. Hence, depending on the specific scenario the assembly process might produce better results if we use the most appropriate assembler. Even though contiguous genomes may not be produced, segments from the reference genomes can be obtained using existing assembly methods. Therefore, the need to evaluate the quality of assemblies exists. These evaluations help researchers to pick different assemblers for different scenarios.

Continue reading Assessing the Quality of Genome Assemblies using QUAST

Metagenomics — Who is there and what are they doing?

Posted on by Vijini Mallawaarachchi

Did you know that your body houses about 100 trillion bacteria? Estimates show that a human has approximately a pound or two of bacteria living in his/her gut (stomach) [1] (Now don’t go and drink all the antibiotics you know, to kill those bacteria. In fact, these bacteria play an important role in our metabolism and immune system). The same goes for the backyard of your house. There can be many species of bacteria living in the soil and they help to enrich the soil (e.g.: nitrifying bacteria produce nitrates which are essential for plants). These microscopic communities have very diverse ecosystems and studying their composition and behaviour can provide us with valuable insights. In this article, I will provide a basic introduction to metagenomics, which is the study of genetic material obtained from microbial communities.

Continue reading Metagenomics — Who is there and what are they doing?

A Dummies’ Intro to Bioinformatics

Posted on by Vijini Mallawaarachchi

The word Bioinformatics is making quite a turnaround in today’s world of Science. The word seems to be made up of two parts which are related to two different fields, biology and computer science. About one or two decades ago, people saw biology and computer science as two entirely different fields. One would learn about living beings and their functions whereas the other would learn about computers and underlying theories.

Continue reading A Dummies’ Intro to Bioinformatics