ABSTRACT itself as an integral component of any

ABSTRACT

                         The pace, by which
scientific knowledge is being produced and shared today, was never been so fast
in the past. Different areas of science are getting closer to each other to
give rise new disciplines. Bioinformatics is one of such newly emerging fields,
which makes use of computer, mathematics and statistics in molecular biology to
archive, retrieve, and analyse biological data. Although yet at infancy it has
become one of the fastest growing fields, and quickly established itself as an
integral component of any biological research activity. It is getting popular
due to its ability to analyze a huge amount of biological data quickly and
cost-effectively. Bioinformatics can assist a biologist to extract valuable
information from biological data providing various web- and/or computer-based
tools, the majority of which are freely available. The present review gives a
comprehensive summary of some of these tools available to a life scientist to
analyse biological data. Exclusively this review will focus on those areas of
biological research, which can be greatly assisted by such tools like analyzing
a DNA and protein sequence to identify various features, prediction of 3D
structure of protein molecules, to study molecular interactions, and to perform
simulations to mimic a biological phenomenon to extract useful information from
the biological data. The functioning and specificity of the tools like,
iTasser, some other softwares and tools given on other pages and these are discussed
in the following review.

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Introduction

                              Bioinformatics is
an interdisciplinary science, emerged by the combination of various other
disciplines like biology, mathematics, computer science, and statistics, to
develop methods for storage, retrieval and analyses of biological data.Paulien
Hogeweg, a Dutch system-biologist, was first person who used the term
“Bioinformatics” in 1970, referring to the use of information technology for studying
biological systems. The launch of userfriendly interactive automated modeling
along with the creation of SWISS-MODEL server around 18 years ago resulted in
massive growth of this discipline. Since then, it has become an essential part
of biological sciences to process biological data at a much faster rate with
the databases and informatics working at the back end. These tools are also
used for the designing of the primer and some other important sequencing like
the DNA and RNA or some protiens sequencing.

                                 Computational
tools are routinely used for characterization of genes, determining structural
and physiochemical properties of proteins, phylogenetic analyses, and
performing simulations to study how biomolecule interact in a living cell.
Although these tools cannot generate information as reliable as
experimentation, which is expensive, time consuming and tedious, however,
the in
silico analyses can still facilitate to reach an informed
decision for conducting a costly experiment. For example, a druggable molecule
must have certain ADMET properties to pass through clinical trials. If a
compound does not have required ADMETs, it is likely to be rejected. To avoid
such failures, different bioinformatics tools have been developed to predict
admit properties, which allow researchers to screen a large number of compounds
to select most drugable molecule before launching of clinical trials. Earlier,
a number of reviews on various specialized aspects of bioinformatics have been
written. However, none of these articles makes it suitable for a scientist who
does not belong to computational biology. Here, we take the opportunity to
introduce various tools of bioinformatics to a non-specialist reader to help
extract useful information regarding his project. Therefore, we have selected
only those areas where these tools could be highly useful to obtain useful
information from biological data. These areas include analyses of DNA
sequences, phylogenetic studies, predicting 3D structures of protein molecules,
molecular interactions and simulations as well as drug designing. The
organization of text in each section starts from a simplistic overview of each
area followed by key reports from literature and a tabulated summary of related
tools, where necessary, towards the end of each section.

i.                  
iTassar

                                 
Iterative Threading Assembly Refinementis a
bioinformatics method for predicting three-dimensional structure model of
protein molecules from amino acid sequences.

Specificity

                        It detects the
structure templates from Protein Data Bank by a technique called
fold recognition or threading. The full-length structure models are
constructed by reassembling structural fragments from threading templates using
Replica Exchange Monte Carlo Simulation. I-TASSER is one of the most
successful protein structure prediction methods in the
community-wide CASP experiments. I-TASSER has been extended for
structure-based protein function predictions, which provides annotations
on ligand binding
site, gene
ontology and enzyme
commission by structurally matching
structural models of the target protein to the known proteins in protein
function databases. It has an on-line server built in the Yang Zhang Lab at the University of Michigan, Ann
Arbor, allowing users to submit
sequences and obtain structure and function predictions. A standalone package
of  I-TASSER is available for download at the I-TASSER
website.

Functioning

The I-TASSER server allows users
to generate automatically protein structure and function predictions.

·        
Input

·        
Mandatory

·        
   Amino acid sequence with length from 10 to
1,500 residues

·        
Optional

·        
   Contact restraints

·        
   Distance maps

·        
   Inclusion of special templates

·        
   Exclusion of special templates

·        
   Secondary structures

·        
Output

·        
Structure
prediction

·        
   Secondary structure prediction

·        
   Solvent accessibility prediction

·        
   Top 10 threading alignment from LOMETS

·        
  Top 5 full-length atomic models

·        
  Top 10 proteins in PDB which are structurally
closest to the predicted models

·        
   Estimated accuracy of the predicted models

·        
   B-factor estimation

·        
Function prediction:

·        
    Enzyme Classification and the confidence
score

·        
    Gene Ontology terms and the confidence
score

·        
     Ligand-binding sites and the confidence score

·        
     An image of the predicted ligand-binding
sites

Conclusion and
Future Prospects

Bioinformatics is a comparatively young discipline and has
progressed very fast in the last few years. It has made it possible to test our
hypotheses virtually and therefore allows to take a better and an informed
decision before launching costly experimentations. Although, more and more
tools for analyzing genomes, proteomes, predicting the structures, rational
drug designing and molecular simulations are being developed, none of them is
‘perfect’. Therefore hunt for finding a better package for solving the given
problems will continue. One thing is clear that the future research will be
guided largely by the availability of databases, which could be either generic
or specific. It can also be safely assumed, based on the developments in the
field of bioinformatics, that the bioinformatics tools and software packages
would be able to give results that are more accurate and thus more reliable
interpretations. Prospects in the field of bioinformatics include its future
contribution to functional understanding of the human genome, leading to
enhanced discovery of drug targets and individualized therapy. Thus,
bioinformatics and other scientific disciplines have to move hand in hand to
flourish for the welfare of humanity. And some other softwares and tools are
given below

·        
Ensamble

·        
Readseq

·        
INSDC

·        
DDBJ

·        
PIR

·        
AceDB

·        
BanKit

·        
Sequin

·        
Spin

·        
Panther

·        
NCBI ORF finder

·        
ORF Predicter

·        
ORF Investigation

·        
RNA Seq

·        
PDB

·        
UniProt

·        
UCSC

·        
Genbank

·        
Expaxy

·        
Ensamble

·        
Readseq

·        
Entrez

·        
Magpie

·        
GenQuiz

·        
GenScan

·        
ORF finder

·        
Modeller

·        
I-Tasser

REFERENCES

Mount DW Sequence and genome
analysis. New York: Cold Spring.

Hesper B, Hogeweg P
Bioinformatica:eenwerkconcept. Kameleon 1:28-9.

Hogeweg P The roots of
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Peitsch MC ProMod and Swiss-Model:
Internet-based tools for automated comparative protein modelling. Biochem
Soc Trans 24: 274-279.

Dibyajyoti S, Bin ET, Swati P
Bioinformatics: The effects on the cost of drug discovery. Galle Med J
18:44-50.

Ouzounis CA, Valencia A Early bioinformatics: the
birth of a discipline–a personal view. Bioinformatics 19: 2176-2190.

Molatudi M, Molotja N, Pouris A Abibliometric
study of bioinformatics research in South Africa. Scientometrics 81:47-59.

Ouzounis CA Rise and demise of
bioinformatics? Promise and progress. PLoS Comput Biol 8: e1002487.

Geer RC, Sayers EW Entrez: making use of its power.
Brief Bioinform 4: 179-184.

Parmigiani G, Garrett ES,
Irizarry RA, Zeger SL. The analysis of gene expression data: an overview
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