Bioinformatics: BioEdit

One of the primary needs of man, in terms of the cognitive and psychological aspects of life, is to understand himself and other forms of life in order to determine each other’s role and place as inhabitants on earth with unique physiological, anatomical, and most importantly in this case, biological features which exhibit major differences from each other, setting the stage for discovering the quintessential facets of life.This particular need of man had been provided for due to the capacity of Science and Technology to allow him to obtain relevant and comprehensive facts that are rational and quantifiable in nature to develop an organized body of knowledge that provides reliable and valid information about human life, as well as other species on the planet, particularly on the measure of how life is formed, transformed, and reproduced.Under these pretexts, the importance of information is framed pertaining to its connection with the field of biology, specifically under the f ramework of Molecular Biology, Genetics, Computer Science, IT, and Statistics. (Ramsden, 2004) Aside from the purpose of collating reliable and valid information to provide man with an open access to facts or data for the purpose of cognitive enlightenment and sustenance of psychological needs, and so on, solving various issues and problems confronting man and other species on earth may also be addressed through the information-gathering process.Not only does it contribute to the field of Molecular Biology or Genetics for instance, but the processes of obtaining pertinent and comprehensive data are advantageous in addressing concerns in various fields, including Health Care and Medicine, Farming, Agriculture and environmental concerns, Nutrition, Food Processing and Production, and so on. (Hyman, 2003) The process of resolving these multiple issues that affect almost all major fields or industries start by focusing attention on gathering and analyzing information which may be initia lly categorized under Molecular Biology, and then subsequently, Genetics.The next step constitutes the synthesis and organization of information in order to develop theoretical approaches and practical strategies for problem-solving purposes. However, positioning the theoretical framework of Molecular Biology into practical environments and realizing its purpose of obtaining information to contribute to various fields and industries have never been easy. One should not expect that gathering information from various life forms is a trouble-free task.Since molecular and biological information covers a vast scope, (Bommarius & Riebel, 2004) and information obtained requires meaningful, factual, and systematic observations, interpretations, analyses, and synthesis, the necessity for developing a tool or a system to manage the various processes involved, such as the information-gathering, the storage and retrieval of data, the management of data, and so on, (Ramsden, 2004) was realized.T hrough the fusion of technology, particularly Information Technology or IT, Computer Science, Statistics, and Molecular Biology, Bioinformatics came about addressing problems that challenged the informational system of Biology. With the development of Bioinformatics, scientists, particularly molecular biologists and geneticists, have founded an efficient way to create a database of pertinent information obtained under the application of Molecular Biology since its inception, wherein facts and data gathered may be stored and organized for future access or retrieval.(Ramsden, 2004) Moreover, through services provided by Bioinformatics, it allows scientists to organize and synthesize information meaningfully for rational and relevant evaluations and assessments of facts in order to arrive at substantial results that lead to the formation of sound conclusions and generalizations. Bioinformatics therefore focus on the organization of facts and data, the synthesis of this information to d evelop bodies of knowledge, and finally, the evaluation and assessment of facts or data in order to formulate pertinent theories and strategies in addressing biological concerns across multiple disciplines.(Bommarius & Riebel, 2004) With these information on Bioinformatics in mind, the remainder of this discussion shall be devoted to discussing the history of Bioinformatics, the role of Computer Science, Information Technology, Molecular Biology, and Statistics in the development, sustenance, functioning, and efficiency of Bioinformatics, and an evaluation of a Bioinformatics tool or software in relation to its goals or objectives, its interface, available application features and characteristics, additional services, and so on.A SHORT HISTORY IN BIOINFORMATICS Due to the influx of information from numerous research studies conducted by scientists under the coverage of Molecular Biology, the ongoing process has fueled the need for the development of a system that shall be able to or ganize and collate information – that is, Bioinformatics.From Tiselius’ design of the process of electrophoresis, to the development of the alpha-helix by Pauling and Corey, and consequently the improvement of Pauling and Corey’s model to the double-helix by Watson and Crick, developments on protein crystallography, the creation of the Advanced Research Projects Agency Network or ARPANET, the creation of molecular models, and so on, these various events and situations were taken collectively developing the need and recommendation for the creation of a model or framework that will handle information simultaneously, efficiently, and reliably.(Sadek, 2004) From the developments and discoveries of new information based on the processes and techniques employed in the field of Molecular Biology, supported by the attention and interest granted to computers and technology during the eighties because of the dawn of the era of technology, the role of Bioinformatics was re alized, emphasized, and consequently developed. Scientists, as well as various organizations, industries, academic institutions, and such, have continued to develop and improve Bioinformatics.The results constitute the engineering of various applications or softwares since the concept of Bioinformatics was framed during the seventies. Each program or application that was structured were designed to carry out multifarious and specific tasks and responsibilities including DNA sequencing or mapping, the organization of data according to priorities, use, needs, concerns, problems, etc. Some of these applications or softwares include the PC/GENE, PROSITE, SEQANALREF, etc.(Agarwal, 200-) At present time, Bioinformatics continue to evolve and develop as man consciously obtains more complex information and experience developments from previous knowledge and established theories or concepts. In addition, as numerous problems and conflicts related to Biology and its practical application incl uding lessons or concepts arise, Bioinformatics as a practical and essential field in Science and Technology will continue to look for solutions in order to address these concerns.The changing landscape of society, particularly its move from traditionalism and individualism to modernization and globalization, influences changes and transformations in Bioinformatics. BIOINFORMATICS: Molecular Biology, Computer Science, IT, and Statistics In order to deeply understand how Bioinformatics work, we need to go over the structure and features of the subfields that it constitutes, such as Molecular Biology, Computer Science, IT, and Statistics. Molecular Biology is a branch of Science that deals with the analysis of various molecules within living things in general.Various types of cells from man, animals, and plants are studied and analyzed in order to determine molecular compositions, and consequently learn determine their structures and compositions, their reactions to other molecules an d substances found within living things, their functions and contributions to human life, or life in general including plants and animals, and so on. Molecular Biology also studies Deoxyribonucleic Acid or DNA compositions of living things as they contribute knowledge and information on Genetics.This particular aspect focuses on structuring how molecules reproduce through DNA replication within a cell. (Hyman, 2003) Computer Science and IT are both products of the fusion between Science and Technology. They function because of the build-up of information that constitutes Molecular Biology for the purposes of quantifying and qualifying facts and data into meaningful sequences, models, or formations that may be interpreted, analyzed, and synthesized.Some of the specific contributions of Computer Science and IT include the storage, construction, and reconstruction of DNA sequences, a thorough genome analysis by accessing various related information in databases managed by IT, the const ruction of graphic organizers or visual representations of information for clarity and direct presentation of facts, the timely and efficient transfer and receipt of information across databases and information systems, and the collation of variable information about protein sequences. (Keedwell & Narayanan, 2005)Statistics, as a mathematical and scientific approach to analyzing and interpreting data, contributes to Bioinformatics by allowing scientists to test the weight or magnitude of information and provide quantifiable data that may be interpreted according to established standards or guidelines. Information, facts, or data, obtained through experiments and consequently, the findings obtained by molecular biologists from thorough analysis and evaluation an in depth research studies are labeled with values leading to the formulation of estimates, predictions, or likelihoods of the occurrence of various phenomena.Moreover, Statistics is important in allowing computers and various technologies to determine how facts or data are to be translated in order to arrive at scientific conclusions of generalizations. (Ramsden, 2004) By and large, the unique features and contributions of these fields in Science, Technology, and Mathematics, meld together in order to build the foundations of Bioinformatics.Information from Molecular Biology are utilized and transformed to numerical data through Statistics, and both informational statements and figures are stored in computers and other technologies including IT systems or processes, IT functions, standards, guidelines, etc. for easy access and retrieval, synthesis, analysis, and interpretation, and are consequently managed through IT systems and processes. BIOEDITBioEdit is a software application made available for Windows Operating Systems that is used to reconstruct how DNA, nucleic acids, and amino acids are arranged in order to follow the superlative sequence of these substances based on rules and standards derived from previous studies and analyses by molecular biologists and geneticists. Aside from these functions, BioEdit also runs to provide users with graphic simulators that construct drawings or illustrations, chartings and mappings, etc. , BLAST searches, and alignments.(Salemi & Vandamme, 2003 and Tsai, 2002) Coverage and Value of BioEdit to Bioinformatics The study of Molecular Biology necessitates the in depth analysis and evaluation of molecules and their various compositions found in living things, particularly proteins or amino acids which were then identified to be the edifices of life. As time passed, molecular biologists realized the importance of going beyond the study of protein or amino acid structures, and focus on DNA and other nucleic acids which map out how life is formed, transformed, or reproduced.The study of the two most important molecular structures in living things – amino acids and nucleic acids – forms the foundation of Molecular Biology, as well a s Genetics, as fields of science. (Horobin, 2003) In studying these acids, molecular biologists and geneticists need to determine their composition, structures, and sequences in order to identify how they are formed and identify their respective roles in building life. (Horobin, 2003) For the purpose of deeply understanding the importance of sequencing and realignment in Molecular Biology, as well as Genetics, we will focus on the subject of DNA.Molecular Biologists and Geneticists utilize the process of DNA sequencing by following established methodologies and standards. Because of enormous funding obtained from both public and private sectors that are extremely interested in advancing the field of genome sequencing, particularly for purposes of genetic modification and cloning, the DNA sequencing methodology has been continuously evolving in order to adapt new findings and trends that raise its reliability, validity, and efficiency. (Griffin & Griffin, 1994)Sequencing and realignm ent of data and samples help Molecular Biologists and Geneticists create various patterns of DNA links or formation, assemble or disassemble structures for a deeper or more thorough analysis, create a map or graphic organizer which will instantly illustrate how enzymes or other substances are formed from base samples such as DNA, analyses of DNA samples and sequences in order to predict outcomes in protein formation, analyses of protein or amino acids in order to determine their specific features or characteristics, look for other structures or sequences within the database with similar characteristics and formations with the sample, and consequently aligning similar structures or sequences together in order to predict reactions, growth and development, and so on. (Griffin & Griffin, 1994)Results from the sequencing, alignment, or realignment processes that are primary accomplished by resorting to bioinformatics tools such as BioEdit, constitute the information for proper DNA sequen ces in order to identify anomalies or flaws in other models or structures. This is most important in the field of medicine and health because it helps professionals determine serious diseases or illnesses that might be passed on through heredity, varying genes in order to alter anomalies or flaws within its structures, and such. Sequences and alignments also help further genetic cloning because it provides relevant information on how life may be reproduced in the process. Other practical uses of DNA sequencing and alignment include the improvement product formation, by determining how the formation of genes may be developed gearing towards constructiveness, particularly in the food industry. (Walker & Rapley, 2000)BioEdit, as a tool for sequencing and aligning various molecules or substances such as DNA, nucleic acids, amino acids, etc. , is therefore extremely important in the realization of the goals of Molecular Biology and Genetics. Through its comprehensive services and feature s aside from sequencing and aligning, the application is able to help molecular biologists and geneticists thoroughly analyze sequences for various purposes aforementioned, consequently advancing not only their respective fields but other scientific industries as well including health care and medicine, psychology and behavior, farming and agriculture, food processing and production, genetics, etc. BioEdit: The ApplicationBioEdit is available for free download from various online sources offering different versions, including tutorials and general databases for the purpose of comparing sequences. For this reason, BioEdit appears to be instrumental in one’s accomplishment of various tasks and responsibilities that are associated to the study of DNA, amino acids, nucleic acids, etc. because the software is readily available for users who need access to such Bioinformatics tools. In addition, there are several online tutorials that will help one in learning how to use the applic ation appropriately and efficiently. For this particular evaluation, BioEdit 7. 0. 9 was used and downloaded from http://www. mbio. ncsu.edu/BioEdit/BioEdit. html. (Hall, 2007) Although there are online tutorials available for new users, handling BioEdit is quite difficult. One cannot easily use BioEdit the first time because there is a need to go over terminologies, exploring the functions and requirements of running BioEdit. For instance, the Accessory Application tab contains various commands or protocols that are unfamiliar to new users, unless they have comprehensive experiences in handling other applications or programs with similar interface. In order to begin working with BioEdit, one must know what BLAST is, CAP or Contig Assembly Program, a Protein Distance Matrix, and so on.Moreover, there is a need for new users to familiarize themselves with various goals and objectives that should be accomplished in using BioEdit in order to determine which tools found in the tabs shal l be used and how databases shall be drawn from the World Wide Web for thorough analysis, alignment, or comparison of sequences. One beneficial attribute of BioEdit include the availability of links to online sets that provide databases such as the Vector Database, the PHYLIP Homepage, the RNase P Database, and so on. In addition, BioEdit allows users to utilize sequences in various formats and read and access numerous sequences that may be imported from other sources. BioEdit does not also limit users to the built-in services that come with the download of the program because it opens itself to upgrades by downloading other complementary or helper applications.When it comes to the actual utilization of tools offered by the BioEdit becomes highly useful because it is able to carry out basic tasks, such as editing of sequences from samples, translating the compositions and formation of sequences, the alignment of sequences to multiple sources, and so on. Although the BioEdit is quite difficult to use in the beginning, going over tutorials and Read Me files from online websites is useful in order to familiarize oneself with the interface of the program. Moreover, it offers various tools that completes several tasks and provides access to numerous databases that may be used for many purposes. The following screenshots were obtained from the website wherein BioEdit was used to fulfill various tasks and functions including Split alignment, Hydrophobicity Plots, and Plasmid drawing and annotation. (Hall, 2007)