Category: bioinformatics

Long sequence reads are no longer less accurate than short reads with advances in third generation sequencing

April 2, 2024

Next generation sequencing technologies which have been at the forefront of genomics in the past decade benefits primarily from the accuracies of short sequence reads. But, short sequence reads suffer from deficiencies in enabling the deciphering of repeats or structural variation regions of the DNA. To this end, third generation sequencing come to the fore … More Long sequence reads are no longer less accurate than short reads with advances in third generation sequencing

Cost of synthesis is the main barrier to longer read RNA-sequencing

March 24, 2024

Modern RNA-sequencing relies on next-generation short read sequencing technologies to profile for the total ensemble of mRNA molecules in the sample. Conceptually, it is a formidable challenge as there are literally millions of mRNA molecules that need to be sequenced. The cost of this endeavour is also hefty. To reduce the cost to a manageable … More Cost of synthesis is the main barrier to longer read RNA-sequencing

RNA-seq is a label-free, unbiased genome scale transcriptome profiling technique

March 21, 2024

Understanding gene expression pattern of cells in different health and disease conditions have evolved from an academic curiosity 20 years ago into an almost essential aspect of many biological research workflows. The reason is our newfound ability at correlating gene expression pattern with cellular behaviour and phenotype. To this end, one technique stands out amongst … More RNA-seq is a label-free, unbiased genome scale transcriptome profiling technique

Reference genome provides genomic loci to align the sequence reads from RNA-seq experiments

February 20, 2024

RNA-seq is a popular and accessible transcriptome profiling method that is increasingly used in biological sciences and medical research. It provides a genome scale unbiased view of the gene expression pattern of the cells and tissues, that help provides a mechanistic perspective to phenotypic behaviour and morphological changes. To analyse such an expansive sequence read … More Reference genome provides genomic loci to align the sequence reads from RNA-seq experiments

Gene expression pattern analysis illuminates diverse aspects of biological function

February 14, 2024

It is common knowledge that the genetic repertoire of an organisms lends unique functions to the species. But, it is less well known that differential gene expression pattern can lead to different morphotypes and phenotypic traits in the same species. At the heart of differential gene expression pattern analysis is that not all genes are … More Gene expression pattern analysis illuminates diverse aspects of biological function

Sequence conservation and gene essentiality endow phylogenetic signals in ribosomal proteins

February 13, 2024

Microbes are invisible to the naked eye, and look similar under the microscope where diverse types of microbes could be classified into a few shape categories. Hence, there is a need for other identification and classification methods to catalogue the rich diversity of microbes on Earth. One approach is molecular phylogeny. In molecular phylogeny, the … More Sequence conservation and gene essentiality endow phylogenetic signals in ribosomal proteins

Genome scale phylogeny

January 15, 2024

Phylogenetic tree is the oft used tool for assessing the evolutionary relatedness between different species as well as probing the provenance of specific proteins. The approach typically requires the collection of relevant gene sequences, which will be put through multiple sequence alignments to yield a map of the differences between gene sequences that is the … More Genome scale phylogeny

Focus on a few biotechnology workhorse and model organisms have led us to neglect the rich microbial diversity represented by environmental microbiology

January 12, 2024

Much of fundamental and applied microbiology research has focused on model organism or biotechnology chassis workhorse. Focus on these organisms comes about due to the availability of tools for interrogating the experimental systems as well as the ability to translate findings from model organism to other species. However, biology is marked by diversity, and while … More Focus on a few biotechnology workhorse and model organisms have led us to neglect the rich microbial diversity represented by environmental microbiology

Data visualization tools have become essential for analysis of large biological dataset

January 8, 2024

Compared to earlier eons in biological research, the advent of sequencing and other omics tools have pushed biological research into the big data era. This contemporary era is characterized by a vast array of structural data with variables and matrixes describing many aspects of biology. Given that the number of dimensions in the dataset is … More Data visualization tools have become essential for analysis of large biological dataset

Bacterial genome could be storage medium for genome of extinct bacteriophages

December 21, 2023

One part of a bacteriophage life cycle is to integrate its genome into the host genome. This occurs when environmental or nutritional conditions are not favourable. Thus, the molecular logic goes that once conditions become more favourable, the integrated phage would mobilize and excise its genome out of the host genome in a replicative cycle … More Bacterial genome could be storage medium for genome of extinct bacteriophages