BIOINFORMATICS APPLICATIONS IN PATIENTS’ MEDICALS

BY
AMADI RICHMAN OGBONDA
richyamadi@gmail.com, richyamadi@yahoo.com
+2348098344373, +2348062527661

SUBMITTED TO
THE DEPARTMENT OF COMPUTER SCIENCE, SCHOOL OF SCIENCE AND
TECHNOLOGY, CAPTAIN ELECHI AMADI POLYTECHNIC
P.M.B. 5936 RUMUOLA, PORT HARCOURT

Abstract
Bioinformatics has played a major role in gene sequencing diagnostics and has been an
essential tool to investigate the genetic causes of disease. With the support of new
technologies and tools, bioinformatics can play an important part in the support and
continued development of precision medicine. Bioinformatics is the combination of biology
and information technology. It is a multidisciplinary area of science combination of
biological computational, mathematical, statistical techniques and information technology.
Using information technology tools, we can analysis biological data sequences.
Bioinformatics also helps in biological algorithm development and suitable data analysis
tools to collect information and make discoveries. In this paper we discussed the roles of
bioinformatics and its tools for biological data analysing using computational and statistical
techniques.in this paper we also discussed various applications of bioinformatics in the fields
of medicine and healthcare in general.

Keywords: Bioinformatics, Biology, Data, Information, Medical, Medicine, Patients etc.

Introduction
Bioinformatics is a field of current interest that came into existence when biology and
information technology (IT) converged to explore the basis of life at large. Present
millennium is likely to see a revolution in clinical practices as research in the field unfolds
genetic information and supercomputers assist in organizing, understanding and analysing
this information for a meaningful purpose. Advances in hardware and software tools have
helped to identify the genetic sequences pertaining to organisms and this unravels gene
expressions for specific diseases.
Bioinformatics has played very important role in developing country in many fields.
Bioinformatics is more significance to analyse and identification of biological data using
computer-based techniques to help understanding biology at the system level, bioinformatics
begins to show promise in unravelling genetic networks. It is more useful in dynamic cell
study. It made positively changes in their genome for disease resistant. Bioinformatics is
more practical in medicine fields such as drug discovery, personal medicine, preventive
medicine, predictive, medicine and gene therapy.
Many applications of bioinformatics in fields of microbial genome such as waste clean-up,
climate change, nanotechnology and biotechnology and alternative energy. It is more
applicable in area of agriculture such as crop improvement, insect resistance improves and
nutritional quality. The integration of bioinformatics impacts on plant science and crop
enhancement area. Many bioinformatics tools and techniques are applied to analysis
biological data and enhancement in genes sequences. Bioinformatics made effective changes
in different branches of science and life science. In future work we will try to enhance the
vitamin level in rice and protein level in wheat using existing and proposed bioinformatics
techniques.
Future of medicine is likely to be based on molecular simulations and 3D structural and
surface analysis of gene expressions to provide for individualized post-natal treatment for
aberrations in hereditary instructions. Although applications of bioinformatics in medicine
have mainly been highlighted in the paper, this science of bioinformatics is applicable to
other relevant fields such as of medical laboratory sciences and environmental sciences. An
overview of the integration between biotechnological components and IT for disease
diagnosis/treatment, DNA sequencing, computational biology, drug design and crime solving
has been elaborated.
In recent years new sciences have risen up due to the demand in understanding more in the
field of bioinformatics. Bioinformatics has been introduced to other fields like microbiology,
computational biology, biochemistry, pharmacy, medical laboratory science and others.
Bioinformatics has made a way for medical researchers to determine the effectiveness of a
particular treatment for a given population or to discover the harmful side-effects of a drug.
Bioinformatics have a huge influence in the medical field and also can play a key role in
other fields like agriculture, livestock and even space explorations. Our contribution in this
paper is to gather all the distributed fundamental information about bioinformatics and
summarize them in a systematic fundamental way, specifically for the enhancement of this
research paper.
Aim and Objectives
The main aim of this research work is to understand the concept of bioinformatics and how it
can be applicable in the field of medicine, more especially patients’ medicals.
The objectives of bioinformatics in terms of medicals include:
 Organising biological data in an easy manner that helps physicians and researchers to
store and access information patients;
 Understanding the reasons for developing softwares that help in the analysis and
management of biological data;
 Uses of biological data in the analysis and interpretation of results in a biological
meaningful manner;
 Assisting researchers in the pharmaceutical industry and physicians in the medical
fields to understand gene structures that will help in detecting and diagnosing disease
like cancers, high blood pressure, brain tumours etc.
Review of Related Literatures
History of Bioinformatics
Health care is becoming an increasingly data-intensive field as doctors and researchers
generate gigabytes of medical data on patients and their illnesses. While a patient visiting the
doctor before 15 years may have only generated a few data points basic information such as
weight, blood pressure, and symptoms a medical encounter today may leave a long trail of
digital data from the use of high-definition medical imaging to implantable or wearable
medical devices such as heart monitors. More importantly, as doctors and hospitals transition
away from paper medical records, this data is increasingly being collected and made available
in an electronic format. The availability of large data sets of digital medical information has
made possible the use of informatics to improve health care and medical research. Often
referred to as “in silico” research, informatics offers a new pathway for medical discovery
and investigation. The field of bioinformatics has exploded within the past decade to keep
pace with advancements in molecular biology and genomics research. Researchers use
bioinformatics to gain a better understanding of complex biological processes by, for
example, analysing DNA sequences or modeling protein structures.
The origin of bioinformatics goes back to Mendel’s discovery of genetic inheritance in 1865.
Since the 1953, big revolution achievements took place by James Watson and Francis Crick
as they determined the structure of DNA. Bioinformatics is by nature a cross-disciplinary
field that began in the 1960s with the efforts of Margaret O. Dayhoff, Walter M. Fitch,
Russell F. Doolittle and others and has matured into a fully developed discipline. In 1960s,
the hard work of bioinformatics research started, symbolized by Dayhoff’s atlas of protein
sequences and the early modeling analysis of protein and RNA structures. After a while, the
term Bioinformatics came to sense and use in around 1990s and was described by the
management and analysis of DNA, RNA, and protein sequence data.
Bioinformatics as a Solution for Clinical Diagnostics
According to Ricardo Jorge Pais, PhD (2020), integrating a large amount of data coming
from high-throughput technologies towards personalised medicine and diagnostics cannot be
possible without using computational approaches to sort out the complexity of processing and
correlating multiple variables at the “omics” level. Bioinformatics is an interdisciplinary field
of biology that is focused on applying computational techniques for the analysis and
extracting information from data coming from biomolecules. Usually, it integrates techniques
from the fields of informatics, computer science, molecular biology, genomics, proteomics,
mathematics, and statistics. Although it started as a field fully dedicated to basic research in
evolution and genetics, it has been evolving in parallel with high-throughput techniques
resulting in the development of many methods and tools that facilitate the interpretation of
“omics” data. In bioinformatics, high-throughput data is processed and analysed
systematically from raw data to the results using pipelines of analysis using the full potential
of computers. Bioinformatic pipelines usually contain multiple steps for data quality
assessment, feature extraction, dimension reduction, biomarker detection and results
generation. This set of analysis is fully automated where the user has no interference but can
play the role of “curator” to check the validation of the outputs (results).
With the evolution of the computational power, bioinformatics gained the potential to tackle
big data and integrate a large amount of data much faster than it is produced, becoming a
solution applying high-throughput techniques in clinical diagnostics and personalised
medicine. For example, some studies have demonstrated that bioinformatic pipelines
developed for the analysis of MALDI-ToF mass spectra can extract diagnostic information
from urine, blood and embryo culture media faster than its capacity of being generated. In
genomics, several bioinformatic pipelines of analysis for NGS, RNAseq and microarrays
have been also developed to extract diagnostic information out of sequencing of virus,
pathological bacteria and cancer biopsies.
Predictive Modelling as a Complementary Diagnostic Tool
According to Ricardo Jorge Pais, PhD (2020), predictive modelling frameworks have been
extensively used for describing physiological systems and diseases. These frameworks use
mathematical models and algorithms for generating predictions about a phenotype or making
reasonable estimates with the available data. The integration of these predictors in
bioinformatic pipelines is fundamental to make accurate classifications of patient’s samples
into the likelihood of having a particular disease or not. This methodology is useful in clinical
laboratories for screening and early detection of genetic or metabolic diseases. Also, this type
of approach allows making estimations of inaccessible body chemistry parameters based on
others, which otherwise are impossible due to experimental constraints or the available
methods are too invasive or expensive.
The development of mathematical models and algorithms that generate robust predictions is a
hard task and requires rigorous validation procedures before a predictor is ready to be
launched into the market. Not many predictors for diagnostics are available to be used or can
be adapted to a given clinical laboratory setting. Thus, model development and optimisation
for each lab would be the ideal scenario. Integrating predictive modelling workflows in
bioinformatic pipelines also facilitate model development by systematising the process of
validation and model selection using the data and metadata.
Several types of models can be used to make diagnostic predictions and the choice depends
on the data available, technology and the nature of the problem. Statistical models based on
known distributions of biomarkers are very common to be used in the diagnostic of a
particular disease. These are easy to implement in bioinformatic pipelines and serve as
complementary information for clinicians.
The implementation of pattern recognition, machine learning and artificial intelligence (AI)
algorithms into bioinformatic pipelines are key to optimise mathematical models towards
meeting more accurate predictions. Importantly, the usage of machine learning and AI
algorithms are essential for the idea of personalised medicine because they enable the fitting
of generic models of disease to each patient scenario and body chemistry.
The deterministic models such as the logical and kinetic modelling frameworks can also be
used for simulation of physiological scenarios and making robust predictions with clinical
applications.
Implementing Bioinformatics in Clinical Laboratories
There is still much to be done for the implementation of the full potential of bioinformatics as
a diagnostic tool in clinical laboratories. This requires a joint effort between clinical
laboratories, healthcare systems, and software companies to make it happen. As initial steps,
clinical laboratories and healthcare systems should start to invest in the following:
 Acquisition of computational resources (high-performance computers and servers).
 Hire bioinformaticians or specialised outsourcing companies.
 Implementation bioinformatic tools specifically designed for each laboratory reality.
 Implementation of predictive models in software applications for clinical diagnostics.
Nevertheless, health organisations should also make an effort to recognise, legislate and
validate most bioinformatics and predictive modelling diagnostic tools. Although, this would
be a big investment in time, money and resources. However, in the future, it would pay off in
terms of the quality of the diagnostic services offered to the populations, making it evolve
towards personalised medicine that is affordable for most people.
Applications of Bioinformatics in Medicine
Bioinformatics is wide used in the various areas of medicine. The following are the
application of bioinformatics in the field of medicine:
Drug Discovery: Infectious diseases are now the world's biggest killers of children and
young adults. "They account for more than 13 million deaths a year - one in two deaths in
developing countries" as stated by the WHO. Most deaths from infectious diseases occur in
developing countries. The cause for this has been attributed to the unavailability of efficient
drugs and if at all available, the high cost associated with those drugs. Development of cheap
and efficient drugs for a disease is one of the major problems faced by mankind. This
problem can be solved by rational drug design using Bioinformatics. Pharmacy industry has
switched from the trial-and-error process of drug discovery to a rational, structure-based drug
design. A successful and reliable drug design process could reduce the time and cost of
developing useful pharmacological agents.
Personal Medicine: Personalized medicine is developing practice of medicine that uses
particular's genetic profile to advice decisions made in favour to the prevention, diagnosis,
and treatment of disease. Information about patient's genetic profile can help doctors to
provide proper medication using the proper dose or regimen. It applied for treatment as
personalized cancer medicine, diabetes-related disease and virus. Personalized medicine can
be defined widely as a model of healthcare that is predictive, personalized, preventive and
participatory. Translational bioinformatics is a field that can help address these challenges
and is defined by the American Medical Informatics Association as the development of
storage, analytic and interpretive methods to optimize the transformation of increasing
voluminous biomedical data into proactive, predictive, preventative and participatory health.
Preventive Medicine: Preventive Medicine is practiced by all physicians to possess their
patients healthy. It is also a unique medical subject affiliated by the American Board of
Medical Specialties (ABMS). Preventive Medicine attentions on the health of individuals,
communities, and defined populations. It is also helpful for the treatment for obesity,
blindness. The Epidemiology Division used research methods to understand the patterns and
causes of health and disease in the population and to transform this knowledge into programs
designed to stop disease. The division has a lengthy history of association in NIH-sponsored
multi-site, longitudinal cohort studies, and its faculty oversees many investigator-initiated,
NIH-sponsored research projects and trials.
Predictive Medicine: Predictive medicine is an area of medicine that involves expecting the
probability of disease and instituting preventive processes in order to either prevent the
disease completely or considerably decrease its influence upon the patient. Techniques and
assays include New-born screening, diagnostic testing, medical bioinformatics, Prenatal
testing, Carrier testing, Preconception testing. New-born screening is a public health program
designed to screen infants shortly after birth for a list of conditions that are treatable, but not
clinically evident in the new born period.
Genome Annotation and Gene Therapy: The regulatory sequence and protein coding can
be achieved using genome annotation. It is the process to identify the locations of all genes,
coding regions and structure of genome. Gene therapy is a new method of drug delivery that
detail lists of synthetic machinery of the patient's cell to create a therapeutic agent. It contains
the efficient introduction of functional gene into the suitable cells of the patient in order to
create sufficient amount of protein encoded by transferred gene so as to exactly and
permanently correct the disorder. Strategies of Gene Therapy classified into three categories:
 Gene addition
 Removal of harmful gene by antisense nucleotide or ribozymes
 Control of gene expression
Comparative Genomics: The Genomic features such as gene, will be compared to determine
the genomic structure and function relation between various biological species. The scientists
use the inter genomic maps to trace the whole path of evolution that occurs in genomes of
different species. The information about the point mutations and large chromosomal
segments can be determined by these maps.
Prediction of Protein Structure: The three-dimensional (3D) structure of protein from its
amino acid can be predicted. It is tough to determine the secondary, tertiary or quaternary
structures of proteins. For this purpose, either the method of crystallography or
bioinformatics tools will be used.
Bioinformatics Tools in Developing Systems and Carrying Out Diagnosis
The bioinformatics tools are the application programs for the saving, modify, retrieving and
analysis of biological data. Factors that must be taken into consideration when designing
these tools are:
1. The end user (the biologist) may not be a frequent user of Information technology
and thus it should be very user friendly.
2. These software tools are available on internet and play important roles in scientific
research community.
The bioinformatics tools may be categorized into following categories:
Homology and Similarity Tools: The term homology means relationship between DNA
sequences or bristle patterns on a fly's nose. Homologous sequences are sequences that are
linked by divergence from a common ancestor. So, the degree of similarity between two
sequences can be measured while their homology is a case of being either true of false. This
set of tools can be used to identify connections between novel query sequences of unknown
structure and function and database sequences whose structure and function have been
elucidated.
Protein Function Analysis: Protein function analysis is Identified and of all functional
elements such as coding and non-coding in a genome. The collection of programs allows you
to make comparison in your protein sequence to the alternative or secondary protein
databases that cover information on motifs, signatures and protein domains. Highly important
hits against these different pattern databases.
Structural Analysis: Using structural analysis, we can compare structures with the known
structure databases. The function of a protein is directly an importance of its structure instant
of its sequence with structural homologs. The importance of a protein's 2D/3D structure is
most important study point of view.
Sequence Analysis: Many sequence analysis tools allow you to analysis on your query
sequence such as identification of mutations, evolutionary analysis, and compositional biases.
The identification of biological properties is search based on specific function of your
sequence.
BLAST: The Basic Local Alignment Search Tool (BLAST) for analysis gene and protein
sequences against others in public databases. BLASTs are also useful for human, microbial,
malaria, and other genomes, and tentative human consensus sequences.
FASTA: FASTA is a search database tool that compares a nucleotide or peptide sequence
with a sequence database based on the rapid sequence algorithm. It was the first and most
useful algorithm for database similarity searching.
EMBOSS: EMBOSS (The European Molecular Biology Open Software Suite) is a latest and
free open-source software analysis package specially developed to analyse the molecular
data. It is combination around hundred programs for sequence alignment, data searching with
sequence patterns, protein motif identification and domain analysis, nucleotide sequence
pattern analysis, codon usage analysis for small genomes, and much more.
ClustalW: ClustalW is multiple sequence alignment programs for DNA and protein
identification. It generates biological suitable or meaningful multiple sequence alignments of
different sequences, calculates the best match for the selected sequences.
RasMol: It is a most powerful research tool. It displays the structure of DNA, proteins and
smaller molecules. Protein Explorer, a derivative of RasMol. It is an easier to use program.
Java in Bioinformatics: Java is platform independence. It plays key roles in bioinformatics.
Many simulators such as computer-based biological simulation technologies and
Bioinformatics Solutions' Pattern Hunter are two examples of Java in bioinformatics.
Software developers use the BioJava library to develop bioinformatic softwares.
Python in Bioinformatics: Python is one of the most important programming languages that
come with very powerful libraries that can assist in developing software tool to analyse
biological data. BioPython project is based on bioinformatics.
Findings
Clinicians and medical researchers believe that healthcare systems would enhance their
performance if integrative diagnostic approaches were implemented. Although these
approaches are advantageous, they are time-consuming, expensive and require complex
interpretation, making it hard to be implemented in clinical laboratories. In the last decade,
high-throughput technologies such as NGS, microarrays, RNAseq and MALDI-ToF have
been evolving and demonstrating in research studies to have an enormous potential to be
applied as integrative approaches in personalised medicine and clinical diagnostics.
In this review, some authors have provided an overview of the current state of bioinformatics
with a particular reference to structural and functional aspects of Genomics and their practical
applications to medical diagnosis and treatment. It has been demonstrated that how
bioinformatics has successfully integrated the knowledge of physical and biological sciences
to enable Information Technology to comprehend the hereditary instructions that make each
of us unique. Global efforts are underway to "find the location of over one Lakh human genes
and to read the entire genetic script. Over 100 billion bits of information about human genes
will become available by the year 2025. Identified SNPs are likely to provide in-depth
understanding and possible treatment for more than 6000 genetic diseases that affect human
kind as well as genetic alterations that increase the risk of developing some common
diseases. Variability in response to pathogenic organisms and polymorphic basis of neoplastic
proliferation and human traits are also likely to be unravelled, for predictive, personalised and
preventive medicine. Future diagnosis and treatment may start with post-natal genotyping to
identify susceptibility or immunity from specific diseases and pathogens. To anticipate the
onslaught of diseases later in life a unique combination of vaccines could be prescribed,
minimising the healthcare hazards due to unnecessary treatment.
Follow-ups by regular medical screening would lead to guidance for nutrition intake and
early detection of any other illnesses. To further minimize the side effects, drug-based
treatments could be tailored specifically to the patient and disease, thus providing cost
effective course of medication. Today bioinformatics is not only associated to organize,
understand and analyse information on biological molecule on a large scale but also has an
added dimension in respect of its impact on clinical medicine.
Conclusion
The development in genetic and diagnosis research are leading us towards customized
medicine, which utilizes a patient's genetic makeup to decide the correct drug for the patient.
As the field of systems biology advances with customized medicine, scientists will have the
capacity to apply tools and innovation to comprehend the ailment system that advances from
the molecular, cellular, tissue, and organ levels to the individual and, at long last, the
populace levels. Bioinformatics discoveries can be converted into advancements that are
received by the healthcare framework and biomedical industry in type of diagnostic kits,
analysis programs, and so on, and forth. With the help of AI now we can classify different
types of bioinformatics data for disease identification and also helps to find the genetical
cause of a particular disease.
With technologies fully implemented in clinical laboratories, it is now very possible to extract
a large amount of information about the genome, transcriptome, proteome, metabolome and
phenome of patients.
In conclusion, this paper gives an overview of this multidisciplinary field, by forming a
unique clear definition that is introduced by the reaction of Biology and Computer Science in
addition to some assessment factors like statistics and mathematics to result into the newly
born field Bioinformatics. Taking advantage of genomic technologies to develop drugs
effectively and target them to the right patients depends on the use of bioinformatics, in its
broadest sense. Bioinformatics is conceptualizing biology in terms of molecules (in the sense
of physical-chemistry) and then applying informatics techniques (derived from disciplines
such as applied math, computer science, and statistics) to understand and organize the
information associated with these molecules, on a large-scale.
Recommendation
Artificial intelligence (AI) is one of advanced technology aimed to replace the partially/fully
human intelligence power. It has gained attention in research related to computational
molecular biology and bioinformatics. The performance and accuracy of AI algorithms are
good for DNA and gene sequencing compared with the other computational algorithms. Shi
et al. explained the importance of AI in gene selection tools to classify the microarray cancer
data. Serra et al. gave the comprehensive review on Machine earning algorithms use in field
of bioinformatics for dimensionality reduction of complex data, feature selection for
assigning biomarker in raw data. Single nucleotide polymorphism analysis and classification
using machine learning. Drug repositioning, classification of patient from neuroimaging data
are the different application of AI in bioinformatics.
I highly recommended the adoption of bioinformatics module programme, and to aim and
equip trainees with a range of knowledge and skills, which are relevant and applicable in
communications within healthcare contexts. Participants will learn how to build high-
performing and engaged healthcare teams, establish and sustain effective clinical
relationships, as well as implement strategies and tools to support patient-centred care.
Additionally, physicians and researchers should understand how to work with patient safety
initiatives at the forefront of care, a major goal of this module will be to help health care
professionals to develop the background knowledge and skills necessary for the specialty of
risk management. This module is focused especially to the communication, ethics and risks
associated with genetic testing and disease risk assessment.
References
Aken B. L et al. (2016) “The Ensemble Gene Annotation System”; Database (Oxford
University, Britain).
Bagga P. S (2012). “Development of An Undergraduate Bioinformatics Degree Program at A
Batley Jacqueline, David Edwards (2016). “The Application of Genomics and Bioinformatics
to Accelerate Crop Improvement in A Changing Climate”. Current Opinion in Plant
Biology, 30:78-81.
Gill S. K., Christopher A. F., Gupta S. K., and Bansal P. (2016). “Emerging Role of
Bioinformatics Tools and Software an Evolution of Clinical Research,” Perspectives
in Clinical Research, vol. 7, pp. 115-122.
Hack C, Kendall G (2013). “Bioinformatics: Current Practice and Future Challenges for
Life Science Education.” BIOCHEM. MOLECULAR BIOL. EDUC. 33:82-85.
Hemlata Archana Tiwari (2015). “Applications of Bioinformatics Tools to Combat the
Antibiotic Resistance”; International Conference on Soft Computing Techniques and
Implementations (ICSCTI) Department of ECE, FET, MRIU, Faridabad, India.
Hong H, Hong Q, Liu J, Tong W, Shi L (2013). “Estimating Relative Noise to Signal in DNA
Microarray Data”. International Journal for Bioinformatics. Res. Appl. 2013; 9:433
448.
Hong H et al. (2013). “Critical Role of Bioinformatics in Translating Huge Amounts of Next
Generation Sequencing Data into Personalized Medicine”. Sci. China Life Sci. 2013;
56:110-118.
Mehmood M. A., Sehar U., and Ahmad N. (2014). “Use of Bioinformatics Tools in Different
Spheres of Life Sciences,” Journal of Data Mining in Genomics and Proteomics, vol.
5, p. 1.
Oyelade O., Soyemi J., Isewon I. and Obembe O. O (2015). “Bioinformatics, Healthcare
Informatics and Analytics: An Imperative for Improved Healthcare System,”
International Journal of Applied Information Systems, vol. 8, pp. 1-6.
Siddharthan N, Raja Prabu M, Sivasankari B (2016). “Bioinformatics in Drug Discovery A
Review”; International Journal of Research in Arts and Science. 2:2.
Ujjawal Kumar, Singh Kushwaha, Indra Deo, Jai Prakash Jaiswal, Birendra Prasad (2017).
“Role of Bioinformatics in Crop Improvement, Global Journal of Science Frontier
Research”: The Agriculture and Veterinary. 17:1, Version 1.0.
Xia X (2017). “Bioinformatics and Drug Discovery,” Current Topics in Medicinal Chemistry,
vol. 17, pp. 1709-1726.