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Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data,especially when the data sets are large and complex. Bioinformatics uses biology,chemistry,physics,computer science,computer programming,information engineering,mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can some times referred to as computational biology,however this distinction between the two terms is often disputed. To some,the term computational biology refers to building and using models of biological systems.
The human genome is a complete set of nucleic acid sequences for humans,encoded as the DNA within each of the 24 distinct chromosomes in the cell nucleus. A small DNA molecule is found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA,such as that for ribosomal RNA,transfer RNA,ribozymes,small nuclear RNAs,and several types of regulatory RNAs. It also includes promoters and their associated gene-regulatory elements,DNA playing structural and replicatory roles,such as scaffolding regions,telomeres,centromeres,and origins of replication,plus large numbers of transposable elements,inserted viral DNA,non-functional pseudogenes and simple,highly repetitive sequences. Introns make up a large percentage of non-coding DNA. Some of this non-coding DNA is non-functional junk DNA,such as pseudogenes,but there is no firm consensus on the total amount of junk DNA.
Genomics is an interdisciplinary field of molecular biology focusing on the structure,function,evolution,mapping,and editing of genomes. A genome is an organism's complete set of DNA,including all of its genes as well as its hierarchical,three-dimensional structural configuration. In contrast to genetics,which refers to the study of individual genes and their roles in inheritance,genomics aims at the collective characterization and quantification of all of an organism's genes,their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn,proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.
In bioinformatics,sequence analysis is the process of subjecting a DNA,RNA or peptide sequence to any of a wide range of analytical methods to understand its features,function,structure,or evolution. It can be performed on the entire genome,transcriptome or proteome of an organism,and can also involve only selected segments or regions,like tandem repeats and transposable elements. Methodologies used include sequence alignment,searches against biological databases,and others.
In genetics,an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts,and were instrumental in gene discovery and in gene-sequence determination. The identification of ESTs has proceeded rapidly,with approximately 74.2 million ESTs now available in public databases. EST approaches have largely been superseded by whole genome and transcriptome sequencing and metagenome sequencing.
Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species,spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach compares two or more genomes to discover the similarities and differences between the genomes and to study the biology of the individual genomes. Comparison of whole genome sequences provides a highly detailed view of how organisms are related to each other at the gene level. By comparing whole genome sequences,researchers gain insights into genetic relationships between organisms and study evolutionary changes. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore,Comparative genomics provides a powerful tool for studying evolutionary changes among organisms,helping to identify genes that are conserved or common among species,as well as genes that give unique characteristics of each organism. Moreover,these studies can be performed at different levels of the genomes to obtain multiple perspectives about the organisms.
Functional genomics is a field of molecular biology that attempts to describe gene functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic projects. Functional genomics focuses on the dynamic aspects such as gene transcription,translation,regulation of gene expression and protein–protein interactions,as opposed to the static aspects of the genomic information such as DNA sequence or structures. A key characteristic of functional genomics studies is their genome-wide approach to these questions,generally involving high-throughput methods rather than a more traditional "candidate-gene" approach.
Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics,ecogenomics,community genomics or microbiomics.
In bioinformatics,k-mers are substrings of length contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis,in which k-mers are composed of nucleotides,k-mers are capitalized upon to assemble DNA sequences,improve heterologous gene expression,identify species in metagenomic samples,and create attenuated vaccines. Usually,the term k-mer refers to all of a sequence's subsequences of length ,such that the sequence AGAT would have four monomers,three 2-mers,two 3-mers and one 4-mer (AGAT). More generally,a sequence of length will have k-mers and total possible k-mers,where is number of possible monomers.
Population genomics is the large-scale comparison of DNA sequences of populations. Population genomics is a neologism that is associated with population genetics. Population genomics studies genome-wide effects to improve our understanding of microevolution so that we may learn the phylogenetic history and demography of a population.
RNA-Seq is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample,providing a snapshot of gene expression in the sample,also known as transcriptome.
Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance,as well as virulence factors (VFs),which enable a microorganism to infect a host and possibly cause disease. This includes studying genomes of pathogens which cannot be cultured outside of a host. In the past,researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms. With newer technology,pathogen genomes can be identified and sequenced in a much shorter time and at a lower cost,thus improving the ability to diagnose,treat,and even predict and prevent pathogenic infections and disease. It has also allowed researchers to better understand genome evolution events - gene loss,gain,duplication,rearrangement - and how those events impact pathogen resistance and ability to cause disease. This influx of information has created a need for bioinformatics tools and databases to analyze and make the vast amounts of data accessible to researchers,and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence.
In molecular biology and genetics,DNA annotation or genome annotation is the process of describing the structure and function of the components of a genome,by analyzing and interpreting them in order to extract their biological significance and understand the biological processes in which they participate. Among other things,it identifies the locations of genes and all the coding regions in a genome and determines what those genes do.
Viral metagenomics uses metagenomic technologies to detect viral genomic material from diverse environmental and clinical samples. Viruses are the most abundant biological entity and are extremely diverse;however,only a small fraction of viruses have been sequenced and only an even smaller fraction have been isolated and cultured. Sequencing viruses can be challenging because viruses lack a universally conserved marker gene so gene-based approaches are limited. Metagenomics can be used to study and analyze unculturable viruses and has been an important tool in understanding viral diversity and abundance and in the discovery of novel viruses. For example,metagenomics methods have been used to describe viruses associated with cancerous tumors and in terrestrial ecosystems.
Single nucleotide polymorphism annotation is the process of predicting the effect or function of an individual SNP using SNP annotation tools. In SNP annotation the biological information is extracted,collected and displayed in a clear form amenable to query. SNP functional annotation is typically performed based on the available information on nucleic acid and protein sequences.
Metatranscriptomics is the set of techniques used to study gene expression of microbes within natural environments,i.e.,the metatranscriptome.
Bacterial phylodynamics is the study of immunology,epidemiology,and phylogenetics of bacterial pathogens to better understand the evolutionary role of these pathogens. Phylodynamic analysis includes analyzing genetic diversity,natural selection,and population dynamics of infectious disease pathogen phylogenies during pandemics and studying intra-host evolution of viruses. Phylodynamics combines the study of phylogenetic analysis,ecological,and evolutionary processes to better understand of the mechanisms that drive spatiotemporal incidence and phylogenetic patterns of bacterial pathogens. Bacterial phylodynamics uses genome-wide single-nucleotide polymorphisms (SNP) in order to better understand the evolutionary mechanism of bacterial pathogens. Many phylodynamic studies have been performed on viruses,specifically RNA viruses which have high mutation rates. The field of bacterial phylodynamics has increased substantially due to the advancement of next-generation sequencing and the amount of data available.
Transcriptomics technologies are the techniques used to study an organism's transcriptome,the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here,mRNA serves as a transient intermediary molecule in the information network,whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology is to understand how a single genome gives rise to a variety of cells. Another is how gene expression is regulated.
Clinical metagenomic next-generation sequencing (mNGS) is the comprehensive analysis of microbial and host genetic material in clinical samples from patients by next-generation sequencing. It uses the techniques of metagenomics to identify and characterize the genome of bacteria,fungi,parasites,and viruses without the need for a prior knowledge of a specific pathogen directly from clinical specimens. The capacity to detect all the potential pathogens in a sample makes metagenomic next generation sequencing a potent tool in the diagnosis of infectious disease especially when other more directed assays,such as PCR,fail. Its limitations include clinical utility,laboratory validity,sense and sensitivity,cost and regulatory considerations.
References
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- ↑ Dashti, Zahra Jalali Sefid; Gamieldien, Junaid; Christoffels, Alan (8 August 2016). "Computational characterization of Iron metabolism in the Tsetse disease vector, Glossina morsitans: IRE stem-loops". BMC Genomics. 17 (1): 561. doi: 10.1186/s12864-016-2932-7 . PMC 4977773 . PMID 27503259.
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- ↑ Mwangi, Sarah; Attardo, Geoffrey; Suzuki, Yutaka; Aksoy, Serap; Christoffels, Alan (22 September 2015). "TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis". BMC Genomics. 16 (1): 722. doi: 10.1186/s12864-015-1921-6 . PMC 4578606 . PMID 26394619.
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- ↑ "SA's top researchers honoured". SAnews. 28 August 2015.
- ↑ "Broad Institute | Fulbright Scholar Program". fulbrightscholars.org.
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