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Quiz on bioinformatics
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1 Chapter 1
1.1 Introduction
1.2 Bioinformatics
The general definition of bioinformatics is a field that uses advanced information and computational techniques to solve complex problems in molecular biology. Bioinformatics uses these advanced computational techniques to manage and extract useful information form the DNA, RNA and protein sequence data being generated and stored in large databases. Certain methods for analysing genomes and protein data have been found to be extremely computationally intensive, providing the need for the use of powerful computers.
In summary, bioinformatics involves the creation of databases algorithms and computational techniques for solving problems in molecular biology and has many practical applications (Luscombe et al. n.d.).
1.2.1 Bioinformatics Research Areas
Bioinformatics is a multi-discipline field of study which include computer science, statistics, mathematics to develop algorithms and systems that are capable of solving molecular biology problems .The primary goal of bioinformatics is to understand and solve complex molecular biology problems. This goal can be achieved by developing and also applying computational techniques and information storage, such as data mining, HCP algorithms and database creation. All these techniques are meant to support multiple areas of scientific research including:
Sequence analysis: these are biological sequence such as DNA, RNA, and protein sequence which are the most fundamental object for a biological system at the molecular level (Rhee & Dickerson 2006). There are tools that are used to extract useful information from these sequences and make meaningful.
Genome annotation: it is a process of attaching biological information to DNA sequences. T...
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...g was the solution to all of the problems. Below there are a set of objectives that will be done on the thesis.
Objective 1– Investigate the evolution of sequence alignment algorithms.
Objective 2 – design a timeline for the sequence alignment algorithms
Objective 3– Investigate the High performance computing techniques.
Objective 4– Design and construct cluster for evaluation of the sequence alignment algorithm.
Objective 5– testing of the performance of the cluster environment.
1.7 Expected results
The main goal of this thesis is to address the need of high performance computing in the field of bioinformatics. A detailed timeline of the sequence alignment algorithms will be presented. The need for high performance computing will be showed by a series of experiments where will be comparing the performance of a personal computer against cluster computer.
"Polymerase Chain Reaction (PCR) Fact Sheet." National Human Genome Research Institute. 10 Dec. 2007. National Institutes of Health. .
Proteogenomics is a kind of science field that includes proteomics and genomics. Proteomic consists of protein sequence information and genomic consists of genome sequence information. It is used to annotate whole genome and protein coding genes. Proteomic data provides genome analysis by showing genome annotation and using of peptides that is gained from expressed proteins and it can be used to correct coding regions.Identities of protein coding regions in terms of function and sequence is more important than nucleotide sequences because protein coding genes have more function in a cell than other nucleotide sequences. Genome annotation process includes all experimental and computational stages.These stages can be identification of a gene ,function and structure of a gene and coding region locations.To carry out these processes, ab initio gene prediction methods can be used to predict exon and splice sites. Annotation of protein coding genes is very time consuming process ,therefore gene prediction methods are used for genome annotations. Some web site programs provides these genome annotations such as NCBI and Ensembl. These tools shows sequenced genomes and gives more accurate gene annotations. However, these tools may not explain the presence of a protein. Main idea of proteogenomic methods is to identify peptides in samples by using these tools and also with the help of mass spectrometry.Mass spectrometry searches translation of genome sequences rather than protein database searching. This method also annotate protein protein interactions.MS/MS data searching against translation of genome can determine and identify peptide sequences.Thus genome data can be understood by using genomic and transcriptomic information with this proteogenomic methods and tools. Many of proteomic information can be achieved by gene prediction algorithms, cDNA sequences and comparative genomics. Large proteomic datasets can be gained by peptide mass spectrophotometry for proteogenomics because it uses proteomic data to annotate genome. If there is genome sequence data for an organism or closely related genomes are present,proteogenomic tools can be used. Gained proteogenomic data provides comparing of these data between many related species and shows homology relationships among many species proteins to make annotations with high accuracy.From these studies, proteogenomic data demonstrates frame shifts regions, gene start sites and exon and intron boundaries , alternative splicing sites and its detection , proteolytic sites that is found in proteins, prediction of genes and post translational modification sites for protein.
Threshold 5 tackles the beginning of life on Earth. This is where any living things are characterized by metabolism, homeostasis, and reproduction. Over time, the genetic makeup of any living thing change so later generations being slightly different. This results into diversification and the evolution of certain species that best suit their environment. However, threshold 5 also deals with the idea of dealing with the “natural world.” It may seem that the environment is almost entirely man-made but the “natural world” is still a huge part of the environment. This can be simple as the earth on the ground, the air that people breathe in, or even the sun that provides the heat and light to the planet. However, as human technology progresses the “natural world” becomes less and less apparent in the world today.
Modern techniques , rather than the gene map , maps the map of the DNA within the gene itself : the positions of short sequences " marker " are used as markers signaling over the cromosssomas . Once a gene is discovered, it is necessary to unravel its base sequence prior to its function being studied . The sequencing has become easier with the development of methods for cloning the DNA - producing large amounts of identical fragments. In the method most widely used DNA sequencing , the chain is denatured into single strands . These are then used as templates for DNA synthesis , but such that replication to as the double helix reaches a certain growth in the mold base . In addition to provide DNA polymerase and the four bases, A - G -C- T, also using small amounts of these dideoxynucleotide bases. This is incorporated , as the normal bases, the double helix growth but prevent the continuation of the chain. The fragments are then separated by gel electrophoresis and the base seq...
This book is about the amazing task of mapping and showing all the sequences of the thousands and thousands of genes in the human body. The book is split up into nine chapters each of which covers a different aspect of this incredible project. The book tells all about almost every aspect of the project. It tells all about the project and what the point is, what has been accomplished so far, and when they expect it to be finished. According to the introduction the project is actually expected to be finished sometime this year.
Over the past few decades, advances in technology have allowed scientists to actively manipulate the genetic sequence of an organism through a process called 'genetic engineering'. Many believe that this is a technique which we should exploit and take full advantage of as, after all, it may be the key to curing many hereditary diseases such as heart disease and cancer. It may very well be the solution to overcoming evolutionary barriers and allow us to breed new species. However, if you consider the unknown consequences we may have to face as a result of our futile experimenting, you would find that messing with a system as intricate as nature for curiosity's sake is hardly justifiable.
The use of genetic sequencing in the medical field has innumerable possibilities; genomic medicine, as this new field is now called, will enable the human race to make immense advances in understanding how our genetic heredity makes us susceptible to some illnesses and immune to others. The detection of diseases with a high rate of heredity is just one facet of the gem that is genomics; once researchers are able to map out all of the vital components and rare alleles that sometimes play a large factor in disease, it will be possible to target these specific gene combinations, functional elements, and alleles. Because of the fact that protein, produced by our cells’ ribosomes, has an effect on the pathways that help express our inherited traits, it is important that we understand the relationship between DNA and protein, and how this affects the phenotype of an individual’s genetic attributes. For example, sickle-cell anemia is caused by a flaw in one nitrogenous base sequence in DNA. This flaw then translates into RNA, then into amino acids that determine the phenotype that the subject will have. The discrepancy in something as minute as a nitrogenous base and one amino acid makes the difference between a healthy, normal life and a life ...
“A gene is a segment of DNA or a sequence of nucleotides in DNA that code for a functional product,” Tortora. Microbiology. p. 575. The syllable of the syllable. These genes not only affect our outlook, but also play a role.
I have always been fascinated by Biology and Computer Science which propelled me to take up my undergraduate studies in the field of Bioinformatics. As a part of my undergraduate curriculum, I have been exposed to a variety of subjects such as “Introduction to Algorithms”, “System Biology”, “PERL for Bioinformatics”, “Python”, “Structure and Molecular Modeling” and “Genomics and Proteomics” which had invoked my interest in areas such as docking algorithms, protein structure prediction, practical aspects of setting and running simulation, gene expression prediction through computational analysis. These fields have both a strong computational flavour as well as the potential for research which is what attracts me towards them.
Firstly, an amount of 40.90 g of NaCl was weighed using electronic balance (Adventurer™, Ohaus) and later was placed in a 500 ml beaker. Then, 6.05 g of Tris base, followed by 10.00 g of CTAB and 3.70 g of EDTA were added into the beaker. After that, 400 ml of sterilized distilled water, sdH2O was poured into the beaker to dissolve the substances. Then, the solution was stirred using the magnetic stirrer until the solution become crystal clear for about 3 hours on a hotplate stirrer (Lab Tech® LMS-1003). After the solution become clear, it was cool down to room temperature. Later, the solution was poured into 500 ml sterilized bottle. The bottle then was fully wrapped with aluminium foil to avoid from light. Next, 1 mL of 2-mercaptoethanol-β-mercapto was added into fully covered bottle. Lastly, the volume of the solution in the bottle was added with sdH2O until it reaches 500 ml. The bottle was labelled accordingly and was stored on chemical working bench.
Cheminformatics term was coined for the first time by F.K. Brown and it's defined as "the field of chemistry that integrates chemical data with analytic and molecular design tools finding the 'best- fitting' compounds to address particular targets". It can be called also "chemoinformatics", "chemioinformatics" or "chemical informatics". In silico techniques are used in cheminformatics for a wide range of applications, such as in rotational drug design or in drug diversity, using the structure for predication of the activity and in virtual screening. This was first applied in the making of the period table
Synthetic biology, also known as synbio, is a new form of research that began in the year 2000. The Action Group on Erosion, Technology and Concentration (ETC Group) says that synthetic biology is bringing together “engineering and the life sciences in order to design and construct new biological parts, devices and systems that do not currently exist in the natural world’ (Synthetic Biology). Synthetic biology is aiming to create safer medicines, clean energy, and help the environment through synthetically engineered medicines, biofuels, and food. Because synthetic biology has only existed for fourteen years, there is controversy involving its engineering ethics. In this literature review, I am going to summarize and correlate the International Association for Synthetic Biology (IASB) Code of Conduct for Gene Synthesis, the impact of synthetic biology on people and the environment, and the philosophical debates.
Many people don't know what biomedical engineers do. A biomedical engineer’s job is actually quite interesting. They analyze and create solutions to improving the quality and effectiveness of patient care. They also design technology to accommodate the needs of people with disabilities. They have a big role in helping people begin new lives. The main job of a biomedical engineer is to help create prosthetic limbs or organs for those who are in need of one.
The myriad mysteries of science can be unraveled by the emerging technologies including Biotechnology. Science has always been my interest and forte thus, the choice of Biotechnology as my academic option was the ideal decision. I had prepared for the highly competitive entrance exam AIET to get admission into the integrated Masters Degree in Biotechnology and Bioinformatics at Dr. D.Y. Patil University and secured 87th all over India rank and was proud to gain admission to this venerated university. The academic curriculum has introduced me to amazing subjects like ‘Microbiology’, ‘Molecular Biology’, ‘Biochemistry’, ‘Genetics’ and ‘Industrial Biotechnology’. Although many seminal biological events have been explained in theory during the past century, the technology to harness their potential for benefiting humankind has only been possible during the past few decades. This is testament to the great improvements in biotechnologies and I am glad to be a part of this grand scientific experience.
Since school days the terms like cell, genes, DNA, protein intrigued me a lot and helped me in realizing the dream of pursuing a career in Biotechnology field that has been making many remarkable achievements. The passion towards biological sciences made me to take B.TECH in Biotechnology in Dr. M.G.R. University.