Comparative Genomics

WHAT IS COMPARATIVE GENOMICS?

How are we similar to other animals? How are we different? These questions are all questions that are asked and answered in the field of comparative genomics. The comparison of different genomes is a very useful process that leads to the comprehension of the evolutionary processes within the genome. In addition, by studying various genomes, we are able to better understand which parts of our genome are critical to function. In addition, by comparing the human and chimpanzee genomes, scientists are able to understand the divergence between the two genomes that have occurred in six million years.

This infographic summarizes the many aspects and applications of comparative genomics. [1]

HOW ARE GENOMES COMPARED?

The first task in comparing the genomes of two species is to sequence the DNA. There are many techniques and methods to efficiently and effectively sequence DNA. READ MORE.

In addition, many computational tools have been developed to analyze and compare DNA sequences. As comparative analysis progresses, these tools become more and more efficient and accurate [1].

The visualization of sequences is one of the hardest tasks of automatic sequence analysis. Since examining and analyzing two long genome regions is highly inefficient when performed manually, internet-based genomic browsers are useful tools in comparative genomics. Due to annotations, genomic browsers contain sequence-based biological information about the genomic regions that can make comparative analysis easier.

Some browsers that are especially helpful in comparative genomics are:

UCSC Browser: This browser is open- sourced online and holds sequences and annotation tools for a large collection of genomes.
Ensembl: The Ensembl project contains sequencing references for the genomic profiles of many vertebrates and eukaryotic species, which is especially helpful in the computational analysis of multiple genomic sets.
MapView: The Map Viewer contains information necessary to understand how to map, view, and sequence genomes.
BlueJay Genome Browser: This tool is especially useful in visualizing multiple genomes to scale. The browser allows users to see the annotated genomes in a visual interface [1].

This image shows the comparisons that can be drawn between various genomes from different organisms [2]

VISTA TOOL SET

The VISTA family of tools is one of the only comparative genomic services that integrates the alignment and visualization of multiple genomes for analysis. The family of tools uses alignment technique and a curve visualization strategy to identify and align sequences. The technology also adds a mapping component for the multiple genomic sequences that are being studied in the analysis. The VISTA family of tools also seeks to accurately predict where functional signals in the genome into consideration such as the site where the transcription factor binds [2].

This image shows one of the genomic visualization tools that is offered as one of the VISTA family tools [3].

The VISTA system of aligning genomes is fundamentally different than other programs that attempt similar tasks because it operates on a global alignment scale. The fact that the VISTA tool software is global means that the algorithms utilized by the program directly deal with rearranging the sequencers in the genome [2].

VISTA is used often by biologists, mathematicians, and bioinformatics scientists to compare gene families as well as to compare whole genomes of different animals.

HOW IS COMPUTATIONAL GENOMICS APPLIED IN COMPARITIVE GENOMICS?

The technology that is developed in the field of bioinformatics and computational genomics is critical in the analyzation of multiple genomes during comparative genomic studies. The automation of computational tools such as VISTA and the other databases is a vital aspect of the comparative genomics process because it allows scientists to do other things and not have to engage in the lengthy and time-consuming process of visualizing, mapping, and manually comparing the genomes by hand. The fact that bioinformatics technology is advanced enough to provide efficient and relevant tools is a big reason that comparative genomics can be so successful [1].

The algorithms and software that are developed by bioinformatic and computational scientists are used constantly to analyze, compare, map and visualize the genomes that need to be studied during comparative genomic research. Therefore, computational genomics plays a critical role in the development of this emerging field of scientific research.

This video provides a summary of many of the aspects of comparative genomics. You can spot some of the bioinformatic tools that are essential to this field of study [1a].