This document provides an introduction to the field of bioinformatics. It discusses how bioinformatics applies computing techniques to analyze large amounts of biological data from fields like molecular biology, medicine, and biotechnology. The document outlines the course contents, which will cover topics like biological databases, gene and protein analysis, phylogenetic analysis, and gene prediction. It provides background on related fields like computational biology, medical informatics, and proteomics. The history of bioinformatics is also summarized, from early genetics and discovery of DNA to advances in computing that enabled large-scale analysis of biological data.
Analysis Analysis Analysis Analysisof the entire entire entire protein protein proteinproteincomplementcomplement complement complement of acell, cell, tissue, tissue, tissue, or organism organism organism under under aspecific, specific, specific, defined defined set of conditions conditions conditions .
• Relies Relies Relies on 3basic technological technological technological technological technological cornerstones cornerstones cornerstones cornerstones
• MethodMethod MethodMethod to fractionatefractionate fractionatefractionate fractionatefractionate complexcomplex complex protein/protein/ protein/ protein/ peptide peptide peptidemixturesmixtures mixtures
• MS to acquire acquire the data data necessary necessary to identify identify identifyidentifyindividual individual individual individualproteins proteins
• Bioinformatics Bioinformatics Bioinformatics Bioinformatics Bioinformatics Bioinformatics Bioinformaticsto analyze analyze and assemble assemble the MS data
introduction,history scope and applications of
relation to other fields , bioinformatics,biological databases,computers internet,sequence development, and
introduction to sequence development and alignment
Proteomics is the study of the proteome, the full protein complement of organisms e.g. plasma, cells and tissue.
Understanding the proteome allows for:
Characterisation of proteins
Understanding protein interactions
Identification of disease biomarkers
Proteomics studies play an increasing role in the field of biology. The use of mass spectrometry (MS) in combination with a range of separation methods is the main principal methodology for proteomics. The two principal approaches to identifying and characterizing proteins using MS are the “bottom-up”, which analyze peptides by proteolytic digestion, and “top-down”, which analyze intact proteins.
Analysis Analysis Analysis Analysisof the entire entire entire protein protein proteinproteincomplementcomplement complement complement of acell, cell, tissue, tissue, tissue, or organism organism organism under under aspecific, specific, specific, defined defined set of conditions conditions conditions .
• Relies Relies Relies on 3basic technological technological technological technological technological cornerstones cornerstones cornerstones cornerstones
• MethodMethod MethodMethod to fractionatefractionate fractionatefractionate fractionatefractionate complexcomplex complex protein/protein/ protein/ protein/ peptide peptide peptidemixturesmixtures mixtures
• MS to acquire acquire the data data necessary necessary to identify identify identifyidentifyindividual individual individual individualproteins proteins
• Bioinformatics Bioinformatics Bioinformatics Bioinformatics Bioinformatics Bioinformatics Bioinformaticsto analyze analyze and assemble assemble the MS data
introduction,history scope and applications of
relation to other fields , bioinformatics,biological databases,computers internet,sequence development, and
introduction to sequence development and alignment
Proteomics is the study of the proteome, the full protein complement of organisms e.g. plasma, cells and tissue.
Understanding the proteome allows for:
Characterisation of proteins
Understanding protein interactions
Identification of disease biomarkers
Proteomics studies play an increasing role in the field of biology. The use of mass spectrometry (MS) in combination with a range of separation methods is the main principal methodology for proteomics. The two principal approaches to identifying and characterizing proteins using MS are the “bottom-up”, which analyze peptides by proteolytic digestion, and “top-down”, which analyze intact proteins.
Lecture delivered by T. Ashok Kumar, Head, Department of Bioinformatics, Noorul Islam College of Arts and Science, Kumaracoil, Thuckalay, INDIA. UGC Sponsored National Workshop on BIOINFORMATICS AND GENOME ANALYSIS for College Teachers on August 11 & 12, 2014. Organized by Centre for Bioinformatics, Department of Zoology, NMCC.
DRUG DESIGN BASED ON BIOINFORMATICS TOOLSNIPER MOHALI
Drug design is a very complex process it takes many more times but using the these specific tools we can reduce complex process and save the time and produce a effective new drug that will be helpful in heath environment.
Mascot is a software package from Matrix Science that interprets mass spectral data into protein identities.
In this presentation we will study about MASCOT and also on how to use it.
Systems biology is the computational and mathematical modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionism) to biological research.
Lecture delivered by T. Ashok Kumar, Head, Department of Bioinformatics, Noorul Islam College of Arts and Science, Kumaracoil, Thuckalay, INDIA. UGC Sponsored National Workshop on BIOINFORMATICS AND GENOME ANALYSIS for College Teachers on August 11 & 12, 2014. Organized by Centre for Bioinformatics, Department of Zoology, NMCC.
DRUG DESIGN BASED ON BIOINFORMATICS TOOLSNIPER MOHALI
Drug design is a very complex process it takes many more times but using the these specific tools we can reduce complex process and save the time and produce a effective new drug that will be helpful in heath environment.
Mascot is a software package from Matrix Science that interprets mass spectral data into protein identities.
In this presentation we will study about MASCOT and also on how to use it.
Systems biology is the computational and mathematical modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionism) to biological research.
Recently, it was reported that the forkhead box O (FoxO) transcription factor promotes human cytomegalovirus (HCMV)
replication via direct binding to the promoters of the major immediate-early (MIE) genes, but how the FoxO factor impacts HCMV
replication remains unknown. In this report, we found that human cytomegalovirus (HCMV), a beta herpesvirus member, could
dramatically induce the expression of FOXOs in the infected human fibroblasts. The induced FOXOs were recruited into the viral
replication compartments (vRC) in the nucleus, especially at the late stage of infection. Suppression of FOXO expression by RNA
interference significantly inhibited HCMV replication, and the production of progeny virus was reduced remarkably.
Mechanistically, FOXO knockdown intensively crippled viral late gene expression at the transcriptional level, while it only
marginally affected viral DNA synthesis. This study highlights how FoxO enhances HCMV gene transcription and viral replication
to promote productive infection
The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying and mapping all of the genes of the human genome from both a physical and a functional standpoint.
Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes
this is done by me and my team mates of Wayamba University Sri Lanka for our project.From now we decided to allow download this file.I would be greatful if you could send your comments..
And I'm willing to help you in similar works.I'm in final year of my degree(.BSc Biotechnology)..
pubudu_gokarella@yahoo.com
What is bioinformatics?
About human genome
Human genome project
Aim of human genome project
History
Sequencing Strategy
Benefits of Human Genome Project research
Disadvantages of human genome project
Conclusion
References
43. What Makes Proteomics Important? Out of the thousands of genes, only a handful actually determine that cell’s structure. Many of the interesting things about a given cell’s current state can be deduced from the type and structure of the proteins it expresses. Changes in, for example, tissue types, carbon sources, temperature, and stage in life of the cell can be observed in its proteins.
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Editor's Notes
An appreciation ___ large amount of information about Living things. Applications of BI to _____molecular biology, medicine, pharmacology, biotechnology, agriculture, forensic science, anthropology etc. A useful knowledge of the techniques by which, through the WWW, we access the data and the methods for their analysis.
A sense of optimism that the data and methods of bioinformatics will create profound advances in our understanding of life, and improvements in the health of humans and other living things.
Molecular biology -Genetics & Protein Biochemistry
Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. [1]
Genomics existed before any genomes were completely sequenced, but in a very primitive state
theories of Heredity Developed his theories through the study of pea pods. Studied them “for the fun of the thing”
This concept was later fully developed into the concept of chromosomes
Studied plant and animal germ cells distinguished between body cells and germ cells and proposed the theory of the continuity of germ plasm from generation to generation (1885) Developed the concept of meiosis
British microbiologist In 1928, Studied the effects of bacteria on mice Determined that some kind of “transforming factor” existed in the heredity of cells Frederick Griffith (1881-1941), British microbiologist who discovered a phenomenon called transformation—meaning an alteration of hereditary characteristics—in the Streptococcus pneumoniae bacterium. Griffith’s work paved the way for later experiments, which proved that deoxyribonucleic acid (DNA) is the material within cells that passes on genetic traits. He is considered by some to be the father of molecular biology. Avery's team purified this substance and found it was pure DNA. Avery published the results of his research in 1944. Transformation is the process by which bacteria take up unpackaged DNA from the environment. Only cells that are “competent” can receive DNA in this fashion. Cells can be made competent, however, via a routine procedure in molecular labs where introduction of foreign DNA into bacteria is fundamental to recombinant DNA technology. In transduction, viruses move DNA from one cell to another.
1980: submission of the whole genome sequence of adenovirus to GenBank(R), the National Institutes of Health genetic sequence database. The submission marks the first time that a new method has been used to sequence a whole genome since Walter Gilbert and Frederick Sanger won the Nobel Prize in 1980 for the invention of DNA sequencing in 1977. The whole genome sequence (GenBank accession nos. AY370909, AY370910, and AY370911) was generated in less than one day using the first technology ever designed to sequence whole genomes, not one gene at a time. More importantly, this was accomplished by using a new platform that is scaleable to larger genomes. The bacteriophages Rt7 and Qβ have RNA as their genetic material. The single stranded RNA contains only three genes, One codes for A protein the second for coat protein, and the third for one of four subunits of replicase. (The other three units of replicase are host proteins). Polyoma or SV40 viruses have 5-10 genes and their chromosomes are only 1.7 microns in length. The single stranded DNA virus ØX174 has DNA which codes for 9 Proteins. The bacterial virus lambda has about 40 genes and T4 has over a hundred genes. The number of genes in viruses ranges from only three in the simplest viruses to about 250 in the most complex ones.
Although there is some relationship between the number of genes and the complexity of an organism there in no strict correlation between apparent genetic complexity and the DNA content per haploid nucleus. Thus some fishes and amphibians contain 10 to 20 times more DNA than humans. Moreover, the size of the genome varies over a 20-fold range within the species of a phylum kilo base pairs = 1000 bp; Mb = mega base pairs = 1000000 bp; 1 million bp GBP: 1000 million bp
Comparative Genomics: the management and analysis of the millions of data points that result from Genomics__ Sorting out the mess Functional Genomics: identifying gene functions and associations Strucutural Genomics: future plans of structural genomics efforts around the world and describes the possible benefits of this research
Recall the concept of differentiation from embryology.
The haploid human genome contains ca. 23,000 protein-coding genes , far fewer than had been expected before its sequencing. [1][2] In fact, only about 1.5% of the genome codes for proteins , while the rest consists of non-coding RNA genes, regulatory sequences , introns , and noncoding DNA (once known as "junk DNA"). [3] Surprisingly, the number of human genes seems to be less than a factor of two greater than that of many much simpler organisms, such as the roundworm and the fruit fly . However, human cells make extensive use of alternative splicing to produce several different proteins from a single gene, and the human proteome is thought to be much larger than those of the aforementioned organisms.[ citation needed ] Besides, most human genes have multiple exons , and human introns are frequently much longer than the flanking exons.[ citation needed ]
Prions epigenetics is the study of heritable changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence, hence the name epi- (Greek: επί - over, above) - genetics . These changes may remain through cell divisions for the remainder of the cell's life and may also last for multiple generations. However, there is no change in the underlying DNA sequence of the organism; [1] instead, non-genetic factors cause the organism's genes to behave (or "express themselves") differently. [2] One example of epigenetic changes in eukaryotic biology is the process of cellular differentiation . During morphogenesis , totipotent stem cells become the various pluripotent cell lines of the embryo which in turn become fully differentiated cells. In other words, a single fertilized egg cell – the zygote – changes into the many cell types including neurons, muscle cells, epithelium, blood vessels etc. as it continues to divide . It does so by activating some genes while inhibiting others
The normal role of Prions is not known. It probably protects cells from injury. All known mammalian prion diseases are caused by the so-called prion protein, PrP . The endogenous, properly-folded, form is denoted PrPC (for c ommon or c ellular ) while the disease-linked, misfolded form is denoted PrPSc (for Sc rapie , after one of the diseases first linked to prions and neurodegeneration.) [9][10] The precise structure of the prion is not known, though they can be formed by combining PrPC, polyadenylic acid, and lipids in a Protein Misfolding Cyclic Amplification (PMCA) reaction. [11] Proteins showing prion-type behavior are also found in some fungi , which has been useful in helping to understand mammalian prions. Interestingly, fungal prions do not appear to cause disease in their hosts and may even confer an evolutionary advantage through a form of protein-based inheritance . [12]