In Silico Approach to Study the Regulatory Mechanisms and Pathways of Microorganisms - Applied Environmental Biotechnology: Present Scenario and Future Trends - page 33

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In Silico Approach to Study the
Regulatory Mechanisms and
Pathways of Microorganisms

Arun Vairagi

Abstract
Metabolic pathways and extreme pathways are the central paradigm of
any life form. The detailed study and analysis of these pathways can yield
better and engineered biological systems. This is the time when con-
ventional methods of studying microorganisms are no longer practiced
because of their limited productivity and higher time consumption. Bio-
informatics has fulfilled the need for high-throughput experimental tech-
nologies, which are reliable and less time consuming too. With the help
of computational biology, it is easy to study the whole microorganism's
metabolic and extreme pathways network and to obtain authentic results.
Some in silico tools are designed to fulfill the need for high-throughput
analysis of different pathways in microorganisms, like metagenome an-
alyzer (MEGAN) which works on short-read data, the Pathways Tool
which helps in constructing the pathway database and the Model SEED,
a resource for the generation, optimization, duration and analysis of ge-
nome-scale metabolic models. Thus, network-based pathways are emerg-
ing as an important paradigm for analysis of biological systems.

Keywords
Bioinformatics · Microbial metabolism · In silico tools · Biological systems

3.1 Introduction

3.1.1 Pathway Analysis

A pathway is a sequence of activities among mol-
ecules in a cell that leads to a certain product or
change in the cell. Such a pathway can activate the
assemblage of new molecules, such as a fat or pro-
tein. Pathways can also turn genes on and off. For a
life form to develop correctly and stay well, many