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<h1>Principles of Bioinformatics</h1>
<p>&nbsp;Bioinformatics is a field that invents methods and computer program for understanding biological data. In this days, there are many programs for analyzing gene expression, protein expression, mapping genes and gene annotation. Due to this many biology field can research conveniently and developed more such as genomics and proteomics.</p>
<h1>Bioprogramming</h1>
<p>&nbsp;Bioprogrmming is a process for making program of bioinformatics.[http://www.fao.org/docrep/s6665e/s6665e03.htm]</p>
<h1>Genomics</h1>
<p>&nbsp;Genomics is discipline of genetics for sequencing, assembling and analyzing the function and structure of entire&nbsp;genomes, not single genes.</p>
<h3>Genome analysis</h3>
<h4h5>DNA sequencing</h4h5><p>&nbsp;First of all, select an organism of interest. Then sequence DNA fragments. There areseveral ways for sequencing DNA fragments; shotgun sequencing[http://en.wikipedia.org/wiki/Shotgun_sequencing], high-throughout sequencing, illumina sequencing[http://en.wikipedia.org/wiki/Illumina_dye_sequencing] and ion torrent[http://en.wikipedia.org/wiki/Ion_semiconductor_sequencing].</p><h5>Sequence assembly</h5><p>&nbsp;After sequencing DNA fragments, next step is assembling DNA fragments to rebuild original chromosome. There are two ways; de-novo assembly[http://en.wikipedia.org/wiki/De_novo_transcriptome_assembly] which assemble without&nbsp;any reference sequences, and comparative assembly which use&nbsp;sequences of&nbsp;similar organism for reference.</p><h5>Annotation</h5><p>&nbsp;Genome annotation is giving some biological&nbsp;information to sequences. Main&nbsp;aspects&nbsp;for genome&nbsp;annotation is&nbsp;finding non-protein coding portion, identifying elements on&nbsp;genome&nbsp;and giving information to elements.</p><h3>Fields of genomics</h3><h5>Functional genomics</h5><p>&nbsp;Functional genomics is&nbsp;a field for&nbsp;studying gene&nbsp;function&nbsp;and interactions.&nbsp;They want to find&nbsp;the relationship between the genome and its phenotype.</p><h5>Structural genomics</h5><p>&nbsp;Structural genomics is&nbsp;a field for studying the three dimensional structure of proteins encoded by genome.</p><h5>Epigenomics</h5><p>&nbsp;Epigenomics is&nbsp;a&nbsp;study about the complete set of epigenetic modifications, such as DNA methylation and histone modification, in the cell.</p><h5>Metagenomics</h5><p>&nbsp;Metagenomics is a study of genetic material of environmental samples.</p>
<h1>Transcriptomics&nbsp;</h1>
<div>&nbsp;Transcriptomics is a study on RNAs, such as mRNA, rRNA, tRNA and non-coding RNA. Usually transcriptomics examine the expression level of RNA and study the function of RNA.</div>
<h3>Analyzing methods</h3>
<p>&nbsp;There is two&nbsp;analyzing methods; microarrarys and RNA-seq.</p>
<h5>Microarrays</h5>
<p>&nbsp;Microarrays is a method which collect RNA fragments on solid surface. On solid surface,&nbsp;DNAs&nbsp;are fragmented and attached. When RNAs are introduced in surface, RNA is attached to its anti-sense DNA fragments. So people can see which part of&nbsp;DNA(gene)&nbsp;is highly expressed and figure out the function.[https://en.wikipedia.org/wiki/DNA_microarray]</p>
<h5>RNA-seq</h5>
<p>&nbsp;RNA-seq, also known as RNA sequencing, is a recently method to analyze the&nbsp;amount of RNA in a specific time by using next-generation sequencing.&nbsp;Fore details, see here;[https://en.wikipedia.org/wiki/RNA-Seq][https://en.wikipedia.org/wiki/DNA_sequencing#Next-generation_methods]</p>
<h1>Proteomics</h1>
<p>&nbsp;Proteomics is a study for proteins in organism, such as studying the structure, function and interaction.</p>
<h3>Techniques</h3>
<h5>Mass-spectrometry</h5>
<p>&nbsp;Mass-spectrometry is a chemical method to identify a molecule by measuring the abundance and mass-charege ratio of molecule.[https://en.wikipedia.org/wiki/Mass_spectrometry] Protein can&nbsp;be&nbsp;also detected by mass-spectrometry, so this technique is used to identify purified proteins, protiein in mixture, the amount of specific protein and the distribution of protein.</p>
<h5>Protein-chip</h5>
<p>&nbsp;Protein-chip is uesd to detect the interaction and activity of proteins and define the function. Since large numbers of protein can use, it can define the function in large scale. Detection is done by probe, which are labled with fluoroscent dye. If there is some reaction between probe and protein, fluoroscent signal are emited.</p>
<h3>Proteomics and Bioinformatics</h3>
<p>&nbsp;Since there are so many proteins and thier data, people made computer programs of to analyze protein data conveniently. Examples are here[https://en.wikipedia.org/?title=Proteomics#Bioinformatics_for_proteomics_.28proteome_informatics.29]</p>
<h3>Proteomics and Genomics-Human Genome Project</h3>
<p>&nbsp;Human genome project is a large scale research project. Its aim are defining DNA sequence of human, find genes and mapping genes in gemone. This project is done in 2004 and people found that human has 3 billion nucleotides and 20,500 genes.[https://en.wikipedia.org/wiki/Human_Genome_Project]</p>
<h1>Epigenomics and&nbsp; Phenomics</h1>
<h3>Epigenomics</h3>
<p>&nbsp;Epigenomics study the epigenetic molecule in a cell, which are DNA methylation, histone modification and RNA interference.</p>
<h4>Techniques</h4>
<h5>ChIp-chip</h5>
<p>&nbsp;ChIp-chip is a combined technique for&nbsp;chromatin immunoprecipitation and DNA microarray. It can detect interactions between proteins and DNA, especially DNA-binding proteins.[https://en.wikipedia.org/wiki/ChIP-on-chip]</p>
<h5>ChIp-seq</h5>
<p>&nbsp;ChIp-seq is another method for detecting DNA-binding protein sites, which is combination of chromatin immunoprecipitation and DNA sequencing.[https://en.wikipedia.org/wiki/ChIP-sequencing]</p>
<h5>Bisulfite sequencing</h5>
<p>&nbsp;Bisulfite sequencing is a technique for detecting DNA methylation pattern. The idea is coming from that bisulfite can change cytosine to uracil but can't change 5-methylcystosine. So by compairing orginal DNA&nbsp;and bisulfite-treated DNA, people can find DNA methylation pattern.[https://en.wikipedia.org/wiki/Bisulfite_sequencing]</p>
<h3>Phenomics</h3>
<p>&nbsp;Phenomics study the phenomenon of a organism in respond to gene mutation and environment change.</p>
<h1>Canceromics and Geromics</h1>
<p>&nbsp;Canceromics is a biological field of studying cancer. And geromics is a biological field of studying aging.</p><h1>What Is Real?</h1><p>&ltnbsp;In case tangible things, real is the thing that&nbsp;references/all people&nbsp;can see directly. For example, since 63 building is in Seoul and we can go to Seoul and see it, 63 building real. However, since&nbsp;we&nbsp;can't see&gtnbsp;http://enalien anywhere, alien is not real. If all the people can see alien directly, then alien changes real.wikipediaIn case of formless thing,&nbsp;such as past people and&nbsp;&nbsp;event, if so many articles state and&nbsp;explain&nbsp;something, then that is considered real.org/wiki/Shotgun_sequencing</p><p>In other words, reality&nbsp;is not&nbsp;absolute concept. Reality can be change relatively.</p>
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