Environmental Engineering Reference
In-Depth Information
• A graphical environment is provided so that
the user can easily interact with the PGDB
• It provides a sophisticated ontology and data-
base API that allows a program to perform
complex queries, symbolic computations and
data mining on the content of the PGDB (Karp
et al.
2002
)
Pathway Tools are the combination of four tools
working on different aspects of the same query.
They are known as the four components of the
complete Pathway Tools software.
The first component is the Pathway/Genome
Navigator which provides query, visualization
and analysis services to PGDBs. It can serve both
as a local application as well as a Web server. It
helps in facilitating information fast, and allows
the scientific community to exhibit information
in various forms such as graphical and to distrib-
ute a PGDB to others via the web. The second
component, known as PathoLogic, has a function
for users to create a new PGDB, which contains
information about genes, proteins and other pre-
dicted metabolic networks of the organism. The
third component is known as the Pathway/Ge-
nome Editor, which provides the facility of edit-
ing the PGDB and its content in an interactive
mode. It has a function for creating new path-
ways and establishing relationships amongst the
newly discovered components. The fourth com-
ponent is Pathway Tool Ontology, which defines
the rich set of classes, attributes and relationships
for high-fidelity modelling of biological data.
(Karp et al.
2002
)
of microbiologists towards many problems has
been changed by the subject of metagenomics,
which redefined the concept of a genome, and
accelerated the rate of gene discovery. (Handles-
man
2004
). In addition, the metagenomic librar-
ies derived from environmental DNA are use-
ful for characterizing uncultured microorgan-
isms. However, conventional library-screening
techniques permit characterization of relatively
few environmental clones. (Sebat et al.
2003
).
Jo Handelsman coined the term in 1998. There
are a vast number of metagenome projects cur-
rently active, producing a huge amount of data
related to DNA. Advances in the throughput
and cost-efficiency of sequencing technology
are fueling a rapid increase in the number and
size of metagenomic datasets being generated.
Researchers are now able to study the DNA of
a wider range of microorganisms and genes on
a more complete and detailed scale. The basic
questions of interest are: which species are pres-
ent in a given environment, and what types of
genes, functions or pathways are present in the
DNA or actually active in the sample? As re-
search begins to answer these basic questions,
the focus will shift to the comparison of differ-
ent datasets, because researchers will want to
determine and understand the similarities and
differences between the metagenomes of differ-
ent environments (Fig.
3.5
).
Metagenomics has been defined as “the ge-
nomic analysis of microorganisms by direct ex-
traction and cloning of DNA from an assemblage
of microorganisms.” (Handelsman
2004
) The
fact which made metagenomics more important
is that 99 % of microorganisms are not cultur-
able. The goal of this new area is to achieve a
better insight into the existence of different va-
rieties of microorganisms. The identification of
these unknown microorganisms obtained from
the environment is done by comparing them
with a known sequence database. Developing
sequencing-by-synthesis technologies with very
high throughput are flagging the way to low-cost
random “shotgun” approaches like MEGAN, a
computer program that allows in silico analysis
of large metagenomic datasets.
3.3
Metagenomics
Metagenomes are studied under this head-
ing, as well as the genetic material obtained
directly from the environmental samples. It is
the analysis of genomes of microorganisms by
direct extraction and DNA cloning from an as-
semblage of microorganisms. The development
of metagenomics stemmed from the ineluctable
evidence that as-yet-uncultured microorgan-
isms represent the vast majority of organisms
in most environments on earth. The approach
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