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DNA Construction Software - J5
#1
DNA construction, which is commonly known as DNA cloning or recombinant DNA technology. It is one of the most important and very useful tools for modern biotechnology, genetic studies, medical research, and the development of advanced biofuels.

Recently Nathan Hillson, a biochemist at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI),has developed the most easy and economic DNA construction software . The name of the DNA construction software program is j5.This also identifies which strategy would be the most cost-effective.

This the only special software package today that both standardizes and cost-optimizes the DNA construction process, this is done by the design of short DNA sequences which are used to join longer sequences together in recombinant DNA processes.Over all this newly developed software , improves the precision, scalability, and cost-effectiveness of DNA construction.

Basic of DNA construction includes the process of physically assembling fragments of DNA sequences. Such kind of constructed DNA are very helpful in developing new medical treatments and for modifying or engineering microbes to proficiently carry out a specific task which may include converting cellulosic biomass into dirt free, green, renewable transportation fuels.

The incorporation of the DNA sequence fragments in the DNA construction process are often referred to as parts. These parts are from different organisms are inserted into a self-replicating genetic element, such as a bacterial plasmid, that will multiply the assembled parts in a host cell. Conventionally, this has been achieved through the use of restriction enzymes for splicing desired DNA sequence fragments, and ligation enzymes for bonding the fragments to plasmid cloning sites.
As the size of the plasmids increases because of the more number of parts being incorporated conventional construction of recombinant DNA assemblies becomes ever more difficult. The whole process must be started all over again for alternate combinations of parts, cloning; every time a different gene or fragment is cloned different pair of restriction sites are being used. This a very exhaustive and time-consuming process. In addition to that the Traditional DNA construction methods result in scars in uncontrolled portions of the DNA.This takes place at DNA fragment junctions that can adversely affect function.

With current DNA construction techniques, a small number of enzymes can be used over and over again, independent of the DNA sequence fragments being assembled, and which enables automation with robotic platforms. However, designing protocols for these modern DNA construction approaches can be as tedious, time-consuming and error-prone as the traditional approach. To prevent these usually outsourcing of DNA portion are done by companies that chemically synthesize long sequences of DNA, this is because they are less costly .

To overcome all these problems j5 software for the DNA construction was developed which provides a single design for the SLIC, Gibson, CPEC and Golden Gate DNA assembly strategies and guides us to determine which can be the best and advantageous for a given construction project.
Hence the j5 software package is a Web-based computer application that automatically designs and optimizes state-of-the-art DNA construction protocols. The main advantage of this program over the conventional methods is that, they determine the optimal flanking sequences that should be attached to each DNA part to produce the desired recombinant DNA within minutes and are also least expensive .these is usually executable by hand or robotics.

The j5 software package controls the DNA sequence at every single base pair which is the ability of combinatorial libraries. Combinatorial libraries are the collections of hundreds to millions of related DNA assemblies, each with a different combination of genes or parts that perform similar functions in different organisms. These libraries allow scientists to choose the most effective genetic combination to get preferred result, e.g., the most efficient production of a biofuel or medication in a given host. No other automated DNA cloning software does this on the same scale and as fast and effectively as j5.

The j5 software package is has a graphical interface that enables users to design a DNA construct or combinatorial libraries though the arrangement of individual part logos that theoretically resemble the underlying DNA sequence. The result obtained or the outputs are in the form of user-friendly spreadsheets that detail the resulting designed experimental protocols which provides instructions that can either be followed by a person in the laboratory or fed directly into a robotic platform for a machine to carry out.

As a result, researchers can direct their resources to investigating their primary interests, rather than preparing the DNA that is merely a tool in their experiments.
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#2
A gene can be cloned by following the different steps of the cloning. Inevitably, the process of gene cloning is not a new one. Most of the people and novice biotechnologists know its basic things but to help you in studying, i would suggest to carefully read the following methods:
To start with the cloning process of a gene , DNA has to be separated from the organism which comprises the needed gene.

The separated DNA is purified and then scattered with certain restriction enzyme. Exactly, restriction enzymes are used with regard to cloning. And, they have the capability to produce staggered cuts in certain squences of the Dna, generating scatters with cohesive ends.

Each scattered Dna has a single and stranded sequence of nucleotides to its ends which has the capability to hybridize with Dna which has been scattered with the same restriction enzyme.

Apart from this the fragments of the Dna are incorporated over Plasmids . Exactly, the kind of plasmid proposed to be used for cloning purpose has one restriction site and when it cleaves the said form of enzyme, it generates the similar cohesive ends which exists in the Dna what is about to clone.

The whole process discussed above ultimately line up the Dna fragments and plasmids and in the end form phosphodiesterbonds.

After going through the above cited processes and methods, you need to go through the second step of cloning which begins with incorporating plasmids in the host cells through transformation. Exactly, each of them contains a vaious segment of the Dna from the genuine organism. And, when they are formed together,the cells represent the entire library of the Dna. After that cells could be plated over argar medium and the colony of cells comprising of the needed gene which is to be clone, could be parted away and separated.
Sasa Milosevic
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DNA Construction Software - J500