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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 subsequent process of analyzing and interpreting data is referred to as computational biology.
The human genome is a complete set of nucleic acid sequences for humans,encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule 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 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 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 field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence,genes,gene order,regulatory sequences,and other genomic structural landmarks. In this branch of genomics,whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. 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 genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences in the aligned genomes and checking to what extent those sequences are conserved. Based on these,genome and molecular evolution are inferred and this may in turn be put in the context of,for example,phenotypic evolution or population genetics.
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 sequencing technique that uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample,representing an aggregated snapshot of the cells' dynamic pool of RNAs,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.
SOAP is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly,alignment,and analysis of next generation DNA sequencing data. It is particularly suited to short read sequencing data.
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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- ↑ DeRaedt, Sarah; Bierman, Anandi; Heusden, Peter van; Richards, Cameron; Christoffels, Alan (March 17, 2022). "microRNA profile of Hermetia illucens (black soldier fly) and its implications on mass rearing". PLOS ONE. 17 (3): e0265492. Bibcode:2022PLoSO..1765492D. doi: 10.1371/journal.pone.0265492 . PMC 8929568 . PMID 35298540.
- ↑ Aparicio, Samuel; Chapman, Jarrod; Stupka, Elia; Putnam, Nik; Chia, Jer-ming (August 23, 2002). "Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes". Science. 297 (5585): 1301–1310. Bibcode:2002Sci...297.1301A. doi:10.1126/science.1072104. PMID 12142439. S2CID 10310355.
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- ↑ "The people's fish: Coelacanth genes get sequenced". May 10, 2013.
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- ↑ Picone, Barbara; Hesse, Uljana; Panji, Sumir; Van Heusden, Peter; Jonas, Mario; Christoffels, Alan (September 29, 2014). "Taste and odorant receptors of the coelacanth--a gene repertoire in transition". Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. 322 (6): 403–414. Bibcode:2014JEZB..322..403P. doi:10.1002/jez.b.22531. PMID 24106203 – via PubMed.
- ↑ Christoffels, A.; Masiga, D.; Berriman, M.; Lehane, M.; Touré, Y.; Aksoy, S. (2014). "International Glossina Genome Initiative 2004–2014: A Driver for Post-Genomic Era Research on the African Continent - PMC". PLOS Neglected Tropical Diseases. 8 (8): e3024. doi: 10.1371/journal.pntd.0003024 . PMC 4140670 . PMID 25144472.
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- ↑ Butler, Declan (January 1, 2004). "African labs win major role in tsetse-fly genome project". Nature. 427 (6973): 384. doi: 10.1038/427384b . PMID 14749791. S2CID 8642083.
- ↑ Dashti, Zahra Jalali Sefid; Gamieldien, Junaid; Christoffels, Alan (August 8, 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.
- ↑ Murungi, Edwin; Barlow, Lael D.; Venkatesh, Divya; Adung'a, Vincent O.; Dacks, Joel B.; Field, Mark C.; Christoffels, Alan (April 1, 2014). "A comparative analysis of trypanosomatid SNARE proteins". Parasitology International. 63 (2): 341–348. doi:10.1016/j.parint.2013.11.002. PMC 3979113 . PMID 24269876.
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- ↑ Mwangi, Sarah; Attardo, Geoffrey; Suzuki, Yutaka; Aksoy, Serap; Christoffels, Alan (September 22, 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. August 28, 2015.
- ↑ "Broad Institute | Fulbright Scholar Program". fulbrightscholars.org.
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