ShinUnBeom
Contents
Principles of Bioinformatics
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.
Bioprogramming
Bioprogrmming is a process for making program of bioinformatics.[1]
Genomics
Genomics is discipline of genetics for sequencing, assembling and analyzing the function and structure of entire genomes, not single genes.
Genome analysis
DNA sequencing
First of all, select an organism of interest. Then sequence DNA fragments. There are several ways for sequencing DNA fragments; shotgun sequencing[2], high-throughout sequencing, illumina sequencing[3] and ion torrent[4].
Sequence assembly
After sequencing DNA fragments, next step is assembling DNA fragments to rebuild original chromosome. There are two ways; de-novo assembly[5] which assemble without any reference sequences, and comparative assembly which use sequences of similar organism for reference.
Annotation
Genome annotation is giving some biological information to sequences. Main aspects for genome annotation is finding non-protein coding portion, identifying elements on genome and giving information to elements.
Fields of genomics
Functional genomics
Functional genomics is a field for studying gene function and interactions. They want to find the relationship between the genome and its phenotype.
Structural genomics
Structural genomics is a field for studying the three dimensional structure of proteins encoded by genome.
Epigenomics
Epigenomics is a study about the complete set of epigenetic modifications, such as DNA methylation and histone modification, in the cell.
Metagenomics
Metagenomics is a study of genetic material of environmental samples.
Transcriptomics
Analyzing methods
There is two analyzing methods; microarrarys and RNA-seq.
Microarrays
Microarrays is a method which collect RNA fragments on solid surface. On solid surface, DNAs 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 DNA(gene) is highly expressed and figure out the function.[6]
RNA-seq
RNA-seq, also known as RNA sequencing, is a recently method to analyze the amount of RNA in a specific time by using next-generation sequencing. Fore details, see here;[7][8]
Proteomics
Proteomics is a study for proteins in organism, such as studying the structure, function and interaction.
Techniques
Mass-spectrometry
Mass-spectrometry is a chemical method to identify a molecule by measuring the abundance and mass-charege ratio of molecule.[9] Protein can be 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.
Protein-chip
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.
Proteomics and Bioinformatics
Since there are so many proteins and thier data, people made computer programs of to analyze protein data conveniently. Examples are here[10]
Proteomics and Genomics-Human Genome Project
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.[11]
Epigenomics and Phenomics
Epigenomics
Epigenomics study the epigenetic molecule in a cell, which are DNA methylation, histone modification and RNA interference.
Techniques
ChIp-chip
ChIp-chip is a combined technique for chromatin immunoprecipitation and DNA microarray. It can detect interactions between proteins and DNA, especially DNA-binding proteins.[12]
ChIp-seq
ChIp-seq is another method for detecting DNA-binding protein sites, which is combination of chromatin immunoprecipitation and DNA sequencing.[13]
Bisulfite sequencing
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 and bisulfite-treated DNA, people can find DNA methylation pattern.[14]
Phenomics
Phenomics study the phenomenon of a organism in respond to gene mutation and environment change.
Canceromics and Geromics
Canceromics is a biological field of studying cancer. And geromics is a biological field of studying aging.
What Is Real?
In case tangible things, real is the thing that all people 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 we can't see alien anywhere, alien is not real. If all the people can see alien directly, then alien changes real. In case of formless thing, such as past people and event, if so many articles state and explain something, then that is considered real. In other words, reality is not absolute concept. Reality can be change relatively.
