Bioinformatics And Genetics

Running head: BIOINFORMATICS AND GENETICS
BIOINFORMATICS AND GENETICS
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1BIOINFORMATICS AND GENETICS
Question 1
1. Bioinformatics is a field of study which interprets biological information using a
combination of subjects like biology, informatics engineering, computer science, statistic
and mathematics. Computational biology on the other hand, is a subject were biologists
use biology based data for the development of algorithms so as to understand the
relationships between various biological systems. Data science is the field of using a
combination of statistics, information technology and statistical methods in order to
interpret and analysis quantitative data.1
2. A gene is the most basis functional and physical form of hereditary information. Proteins
are known as the body’s building blocks and muscle building and repairing nutrients.
Genome means a group of chromosomes which are present in every cell of an organism.
A transcriptome are messenger RNA molecules which are expressed by any organism. A
proteome defines a complete group of proteins which are expressed by organisms, tissues
and cells. Genomics is the subject of studying the genomes of a organism.2
3. Comparative genomics is a subject where genomes from various organisms are
researched and compared with each other. Metagenomics is a field where genetic
materials extracted from the environment are researched. The Earth Genome Project is a
program where all the genomes of Earth’s species will be catalogued and sequences
within the next 10 years.3
1 Ranganathan, Shoba, Kenta Nakai, and Christian Schonbach. Encyclopedia of Bioinformatics and
Computational Biology: ABC of Bioinformatics. Elsevier, 2018.
2 Davalos, Veronica, Anna Martinez-Cardus, and Manel Esteller. "The epigenomic revolution in breast
cancer: from single-gene to genome-wide next-generation approaches." The American journal of pathology 187, no.
10 (2017): 2163-2174.
3 Lewis, Ricki. Human Genetics: The Basics. Garland Science, 2016.

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4. A genetic code is triplet means that it can code of 64 combinations in sets of 4 x 4 x 4
after which, this information can be used by DNA to express the placement of 20
essential amino acids. According to the Chargaff’s rule, the ratio of pyrimidine and
purine bases in every DNA should be 1:1 and the amounts of adenine to thymine and
guanine to cytosine should be equal. According to the nucleotide colinearity rule, one
sequence of nucleotides should be arranged in a linear order same as that of another
sequence. The wobble position effect can be seen in a codon’s 3rd nucleotide where the
bind between the mRNA and tRNA does not follow Watson-Crick base pairing.4
5. Basic Local Alignment Search Tool (BLAST) is a programme for finding similarity
between the local regions present in a nucleotide or protein sequences and some of its
types include: Primer-BLAST, SmartBlast, Protein Blast, Nucleotide BLAST, igBLAST
and MOLE-BLAST.5
6. Clustal Omega suite is a programme which can be used to produce alignments between
three sequences or more and its types of output formats include: ClustalW with character
counts, NEXUS, ClustalW, SELEX, STOCKHOLM, VIENNA etc.6
7. The National Center for Biotechnology Information is an organization which provides
information on biomedical sciences, health and genomics. ExPASy is a research portal
which provides access to various scientific and biology based databases. The EBI is a
European based laboratory which specializes in life sciences. The Conserved Domains
and Protein Classification provides a collection of alignment models of multiple
sequences for proteins of full length as well as ancient domains. The VEuPathDB is an
4 Chevance, Fabienne FV, and Kelly T. Hughes. "Case for the genetic code as a triplet of
triplets." Proceedings of the National Academy of Sciences 114, no. 18 (2017): 4745-4750.
5 Shah, Nidhi, Michael G. Nute, Tandy Warnow, and Mihai Pop. "Misunderstood parameter of NCBI
BLAST impacts the correctness of bioinformatics workflows." Bioinformatics 35, no. 9 (2019): 1613-1614.
6 Sievers, Fabian, and Desmond G. Higgins. "Clustal Omega for making accurate alignments of many
protein sequences." Protein Science 27, no. 1 (2018): 135-145.

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ontology based application programme helping in encoding the data present in
information resources located in the Eukaryotic Pathogen, Host & Vector Genomics
Resource.7
Question 2
1. The key drivers and triggers of the biomedical science revolution are: discovery of a sun
centered solar system by Galileo and Copernicus, publication of Newtons’s ‘Principa’ as
well as the works of Francis Bacon and Alexander Koyre.8
2. The main biotechnological advances which led to the 21st Century mixomics/genomics
revolution are: the emergence of robotics, discovering water in planets like Mars,
understanding cancer patients’ genome sequencing, using stem cells to create organs and
the identification of gravitational waves.9
3. We need ethics in biomedical and genomic research for preventing exploitation of
research subjects as well as for protecting the rights and private health data of
participants.10
4. Two main types of cells based on genetic material and organization are prokaryotic
(single celled) and eukaryotic cells (found in multicellular organisms).11
5. The 1950s and 1980s are considered the golden era of modern biology and bioinformatics
due to discoveries like the Chargaff’s Rule, Watson and Crick models in the 1950s as
7 Varki, Ajit. "New and updated glycoscience-related resources at NCBI." Glycobiology 27, no. 11 (2017):
993-993.8 Schork, Nicholas J. "The big data revolution and human genetics." (2018): R1-R1.
9 Conley, Dalton, and Jason Fletcher. The Genome Factor: What the social genomics revolution reveals
about ourselves, our history, and the future. Princeton University Press, 2018.
10 National Academies of Sciences, Engineering, and Medicine. Human genome editing: science, ethics,
and governance. National Academies Press, 2017.
11 Sieber, Karsten B., Robin E. Bromley, and Julie C. Dunning Hotopp. "Lateral gene transfer between
prokaryotes and eukaryotes." Experimental cell research 358, no. 2 (2017): 421-426.

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well as the discovery of nanotechnology, cloning and the Human Genome Project in the
1980s and 1990s.12
6. The biological significance of human genome sequencing, which was discovered in the
Human Genome Project, include: helping researchers to understand genotyping and
genetic transmission of diseases, gene mutations and their relationship with cancer as
well as the various stages of human evolution and bioanthropology.13
Question 7
 The double helical structure of a DNA has molecular and biological significance since it
allows the DNA to be packed tightly to form chromosomes. It also provides a stable
backbone upon which other molecules can attach to the DNA strand.14
 As per this equation in Chargaff’s rule, the ratio of adenine + thymine/ guanine +
cytosine is not equal to 1, however, the ratio between adenine and thymine and guanine
and cytosine is always 1:1 within a species.15
 There are different levels of protein structure and folding since each structure determines
the sequencing of amino acids in a protein, which in turn help a protein to be stable and
also perform functions like muscle contraction of transporting nutrients from one part of
the cell to another.16
12 Jayaraj, Sebastian, and Michelle Gittelman. "Scientific breakthroughs and patent scope: The impact of
the human genome project on early stage drug patents." In 78th Annual Meeting of the Academy of Management,
AOM 2018. 2018.
13 Jayaraj, Sebastian, and Michelle Gittelman. "Scientific breakthroughs and patent scope: The impact of
the human genome project on early stage drug patents." In 78th Annual Meeting of the Academy of Management,
AOM 2018. 2018.
14 Wang, Guliang, and Karen M. Vasquez. "Effects of replication and transcription on DNA structure-
related genetic instability." Genes 8, no. 1 (2017): 17.
15 Rosandić, Marija, Ines Vlahović, Matko Glunčić, and Vladimir Paar. "Trinucleotide’s quadruplet
symmetries and natural symmetry law of DNA creation ensuing Chargaff’s second parity rule." Journal of
Biomolecular Structure and Dynamics 34, no. 7 (2016): 1383-1394.
16 Ovchinnikov, Sergey, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A. Pavlopoulos, David
E. Kim, Hetunandan Kamisetty, Nikos C. Kyrpides, and David Baker. "Protein structure determination using
metagenome sequence data." Science 355, no. 6322 (2017): 294-298.

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References
Chevance, Fabienne FV, and Kelly T. Hughes. "Case for the genetic code as a triplet of
triplets." Proceedings of the National Academy of Sciences 114, no. 18 (2017): 4745-4750.
Conley, Dalton, and Jason Fletcher. The Genome Factor: What the social genomics revolution
reveals about ourselves, our history, and the future. Princeton University Press, 2018.
Davalos, Veronica, Anna Martinez-Cardus, and Manel Esteller. "The epigenomic revolution in
breast cancer: from single-gene to genome-wide next-generation approaches." The American
journal of pathology 187, no. 10 (2017): 2163-2174.
Jayaraj, Sebastian, and Michelle Gittelman. "Scientific breakthroughs and patent scope: The
impact of the human genome project on early stage drug patents." In 78th Annual Meeting of the
Academy of Management, AOM 2018. 2018.
Lewis, Ricki. Human Genetics: The Basics. Garland Science, 2016.
National Academies of Sciences, Engineering, and Medicine. Human genome editing: science,
ethics, and governance. National Academies Press, 2017.
Ovchinnikov, Sergey, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A.
Pavlopoulos, David E. Kim, Hetunandan Kamisetty, Nikos C. Kyrpides, and David Baker.
"Protein structure determination using metagenome sequence data." Science 355, no. 6322
(2017): 294-298.
Ranganathan, Shoba, Kenta Nakai, and Christian Schonbach. Encyclopedia of Bioinformatics
and Computational Biology: ABC of Bioinformatics. Elsevier, 2018.

7BIOINFORMATICS AND GENETICS
Rosandić, Marija, Ines Vlahović, Matko Glunčić, and Vladimir Paar. "Trinucleotide’s quadruplet
symmetries and natural symmetry law of DNA creation ensuing Chargaff’s second parity
rule." Journal of Biomolecular Structure and Dynamics 34, no. 7 (2016): 1383-1394.
Schork, Nicholas J. "The big data revolution and human genetics." (2018): R1-R1.
Shah, Nidhi, Michael G. Nute, Tandy Warnow, and Mihai Pop. "Misunderstood parameter of
NCBI BLAST impacts the correctness of bioinformatics workflows." Bioinformatics 35, no. 9
(2019): 1613-1614.
Sieber, Karsten B., Robin E. Bromley, and Julie C. Dunning Hotopp. "Lateral gene transfer
between prokaryotes and eukaryotes." Experimental cell research 358, no. 2 (2017): 421-426.
Sievers, Fabian, and Desmond G. Higgins. "Clustal Omega for making accurate alignments of
many protein sequences." Protein Science 27, no. 1 (2018): 135-145.
Varki, Ajit. "New and updated glycoscience-related resources at NCBI." Glycobiology 27, no. 11
(2017): 993-993.
Wang, Guliang, and Karen M. Vasquez. "Effects of replication and transcription on DNA
structure-related genetic instability." Genes 8, no. 1 (2017): 17.