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Introduction to Pharmaceutical Biotechnology, Volume 2 (Second Edition)
common in subcellular proteomics. Fluorescence-assisted organelle sorting is a
relatively new technology that employs fluorescence to sort and isolate certain
organelles for proteome research. This method makes it possible to extract very pure
organelles, which significantly facilitates the following analysis of their proteome.
There are a number of spatial proteomics approaches that may be used to analyze
protein distribution, abundance, and localization in different cellular compartments.
Fluorescent imaging, protein proximity tagging, organelle purification, and cellularwide biochemical fractionation are all examples of such techniques. The spatial
organization of proteins inside a cell may be seen in a variety of ways, depending on
the method used [155]. It is crucial to assess and confirm the results of the subcellular
proteome analysis utilizing methods such as multiple reaction monitoring, RNA
interference, and microscopy. These validation processes aim to confirm the
accuracy and dependability of the results obtained from the subcellular proteomic
analysis [156].
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IOP Publishing
Introduction to Pharmaceutical Biotechnology, Volume 2
(Second Edition)
Enzymes, proteins and bioinformatics
Ahmed Al-Harrasi, Saurabh Bhatia and Ajmal Khan
Chapter 9
Bioinformatics
9.1 Introduction
According to the Oxford Dictionary, bioinformatics involves conceptualizing
biology in terms of molecules and applying informatics techniques to understand
and organize the information associated with these molecules, on a large scale. In
brief, bioinformatics is a management information system for molecular biology and
has many practical applications.
Bioinformatics analysis involve:
• the assembly of sequenced data (directly from environmental samples) in
order to construct contiguous sequences (contigs and scaffolds);
• the prediction of genes (and putative proteins) based on the assembled data;
and
• prediction of domains, functions and pathways for the putative proteins.
Bioinformatics is a discipline related to the exploitation and application of computer
hardware and software to the procurement, storage, investigation and imaging of
biological material (figure 9.1)[1]. Scientific developments in recent years have
encouraged marked progress in understanding the genetic basis of phenotypes. With
these advances, genomics has tremendously transformed the scope of biological
problems at a genome-wide scale, exploring vast data and opening numerous
possibilities [2]. However, the enormous amount of information that has been
produced increases the challenges that must be overcome for storage (Moore’s law)
and the processing of biological information. Bioinformatics and computational
biology have been pursued to overcome such challenges [3]. A general scheme of the
process of bioinformatics is shown in figure 9.2.
Bioinformatics has the following three main components:
doi:10.1088/978-0-7503-5387-8ch9 9-1 ª IOP Publishing Ltd 2024. All rights,
including for text and data mining (TDM), artificial intelligence (AI) training, and similar technologies, are reserved.
Introduction to Pharmaceutical Biotechnology, Volume 2 (Second Edition)
Figure 9.1. Bioinformatics: genomic material is sequenced and processed using assembly, gene prediction and
gene annotation tools. Finally, the results are pooled by scientific groups around the world.
• New algorithms and statistics production for evaluating the connections
among large sets of biological data, e.g. DNA sequence data.
• Application of these techniques for the examination and understanding of
different biological data, including nucleotide sequences, amino acid sequences, etc.
• The production of systems for effective storage, access and management of a
large body of varied biological information.
The field of bioinformatics first developed for the production of amino acid sequences
of proteins and nucleotide sequences of DNA. Zuckerkandl and Pauling (1962)
predicted that the amino acid sequences of proteins could be employed to investigate
the evolutionary relationship between different organisms [4]. This suggestion was
based on the evidence that the amino acid sequences of homologous proteins, i.e.,
proteins having similar functions, were related. This started a new area of investigation known as ‘molecular evolution’. Subsequent studies have allowed inferences
of evolutionary relationships from the relative analysis of amino acid sequences of
functionally related proteins. These investigations became possible due to the
development of quantitative procedures for sequence comparisons.
9.2 History of bioinformatics
The first complete assortment of amino acid sequences was collected in the Atlas of
Protein Sequence and Structure by the National Biomedical Research Foundation
(USA). This assortment was modified by Margaret Dayhoff in 1965–78 [2]. Dayhoff
9-2