Over the years scientist and researchers have made tremendous efforts through various inventions and innovation to make life better. Bioinformatics as an interdisciplinary approach has created numerous opportunities in scientific advancements and promoted efforts towards the realization of better living. A considerable milestone development in bioinformatics goes down to the necessary level of life: genes. Previously identification and ability to distinguishing genes were limited hindering scientific manipulations and diagnostic procedures. With a clear understanding of the gene sequencing process, we can surely achieve massive success in the management of various conditions and generally maintaining a healthy generation. Gene annotation has made this to be in reach.
What is gene annotation?
In molecular biology, genomes make the basic genetic material and typically consist of DNA. Whereby, genome include the genes (coding) and the non-coding regions, of interest to us, are the coding regions as they actively influence basic life processes. The genes contain useful biological information that is required in building up and maintaining an organism. Gene annotation can be defined merely as the process of making nucleotide sequence meaningful. However, it’s a much complex process encompassing several procedures and a broad range of activities.
Gene annotation involves the process of taking the raw DNA sequence produced by the genome-sequencing projects and adding layers of analysis and interpretation necessary to extracting biologically significant information and placing such derived details into context. Through the aid of bioinformatics, there exists software to perform such complex procedures. The first gene annotation software system was developed in1995 at The Institute for Genomic Research, and this was used to sequence and analyze the genes of the bacterium Haemophilus influenza.
As a process of identification of gene location and coding regions, gene annotation helps us have an insight of what these genes do in the body by establishing structural aspects and relating them to functions of different proteins. Currently, the process is automated, and the National Center for Biomedical Ontology have a database for records and to enable comparison.
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How is gene annotation performed?
Gene annotation can either be manual or electronic with the aid of tools developed by an amalgamation of organizations. The downsides of the manual technique are that it is time-consuming and the turn-over rate is much low. However, it remains useful for predictive purposes thus serves a complementary function. There exist three main steps in the process of gene annotation:
Identification of the non-coding regions of the genome (exons). This is vital to limit the range of analysis and only focus on the essential components as it is needless doing the tedious work on portions that give no or little biological information.
Gene prediction; these give an overview of the amino acid components of the genes and the role of such elements. Also referred to as gene finding, this process identifies regions of genomic DNA that encode genes. Empirical methods or Ab Initio methods can do it.
Establishing a connection and a correlation between the identified elements and the biological information at hand. Linking of biological functions and data is possible this way.
Homology-based tools for example Blast has hugely simplified the process of gene annotation, and this can now be done without much hassle as witnessed in manual methods that require human expertise.
Modalities of gene annotation
Genomics is a broad study and can be subdivided as structural genomics, functional genomics, and comparative genomics to leverage the understanding of this crucial topic. Similarly, gene annotation exists as a double-phased entity comprising of structural gene annotation and functional gene annotation.
The initial process in gene annotation and involve identification by physical appearance, chemical composition, molecular weight variations, and general morphology. Such differences as coding regions, gene structures, ORFs and their locations, as well as regulatory motifs, are crucial information that is derived from this procedure and influence the process of gene identification as well as distinction. The accuracy of this process can be evaluated based on two parameters; specificity and accuracy. Where sensitivity is the percentage of right signals predicted among all possible correct strengths while specificity refers to the proportion of right signal among all that are forecasted.
The process of relating crucial biological functions to the genetic elements as depicted in the structural annotation step. Biochemical functions, physiological functions, involved regulations and interactions atop expressions are some of the critical roles that are often considered in DNA annotation.
The above steps can involve biological experiments as well as in silico analysis mimicking the internal conditions. A new method seeking to improve genomics annotation-Proteogenomics is currently in use, and it utilizes information from expressed proteins, such information is obtained from mass spectrometry.
Gene annotation is a purposeful process, and some of the vital information that we seek to extract from this process include; CDs, mRNA, Pseudogenes, promoter and poly-A signals, mcRNA among others. Such elements are minute and identification may be hectic. Scientists have developed software and tools to aid the process and notable tools frequently used are; ORF detectors, promoter detectors and start/stop codon identifiers. Automation of this process has created enhanced accuracy, and now there exist large discrepancies between with the manually conducted procedures as gene sequencing is a dynamic topic.
After a successful gene annotation process, it is expected that the obtained information should be published, stored in the database and shared for research purposes.
Gene annotation is a new and exceedingly promising idea, much remains unfolded, and there is a lot of potentially beneficial areas that remains to be explored. Fortunately, many groups have invested in gene annotation, and new developments arise daily. Some of the ongoing projects on gene annotation include; Ensembl, GENCODE and GeneRIF among others. It is important to appreciate that modern literature gets published daily concerning this topic and it is prudent to keep updated.
DNA annotation reveals much of the information contained in the genomes therefore complete gene annotation is descriptive of organisms being and thus remains a milestone invention.