ASSIGNMENT computer-based tools, most of them are

ASSIGNMENT

GULSHAN SARFRAZ

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                                    MC170200950

                                     BIF 401

     Write a review article on different
bioinformatics tools (Tools and software’s name and its specificity and
functioning) that you studied in BIF-401.                          

Abstract

In
the past, the scientific knowledge is being produced and shared today, it was
never being fast. When different areas of science are getting comes to each
other to they give rise to new disciplines. Bioinformatics is a developing
fields, which makes use of computer, mathematics and statistics in molecular
biology to archive, retrieve, and analyse biological data. It has become one of
the fastest growing fields, and it has rapidly established itself as an important
component of any biological research activity. It is very popular due to its
ability to study large amount of biological data rapidly and economically. It can
support a biologist to abstract valuable information from biological data
providing various web- and/or computer-based tools, most of them are freely
available. The present review focus on the complete summary of some of these
tools that is available to a life that give scientist to analyse biological
data. These review will focus on that areas of biological research, those can
be supported by such tools like analysing a DNA and protein sequence to distinguish
features, prediction of 3D structure of protein molecules, it is to study of
molecular interactions, and it is perform biological phenomenon to cutting
useful information from the biological data.

Introduction

 The Bioinformatics is an
interdisciplinary science, It is developed by the combination of various other
disciplines like mathematics, biology, statistics and computer science for the
develop methods for storage, recovery and studies of biological data 1.
Paulien Hogeweg, he was a Dutch system-biologist, it was the first he used
“Bioinformatics” term in 1970, he stating to the use of information technology
for studying biological systems 2,3. The launch of customer friendly
cooperative automatic modelling that is along with the formation of SWISS-MODEL
server around 18 years ago 4 it resulted in enormous growth of this
discipline. It was become an important part of biological sciences that is
method of biological data at a much faster rate with the
databases and informatics working at the backend. There  are 
many  tools  are 
used  in  bioinformatics  in 
our  course  we 
studied  yet .

Some
tools are homology  or  similar tools, protein functional  tools ,sequence  analysis 
tools ,miscellaneous  tools. Homologus
tools  is a similarity  between 
sequence  can  be measured 
true  or a false. PROTEIN 
FUNCTION TOOLS is  used  to compare the sequence  of 
proteins  that it is  to analyse the  protein analysis .STRUCTURE  ANALYSIS tool 
is  used  to evolutionary  analysis 
to determine the  2d or 3d  structure of 
protein. SEQUENCE ANALYSIS tool is used to find out the mutation
and  hydropathy region. EXAMPLE
OF SOME TOOLS

BLAST

FASTA

EMBOSS

CLUSTALW

RASMOL

PROSPECT

PATTERN
HUNT

COPIA

Some
software are  used  in 
this  field  they 
are given below

            Fastpcr

Autoprime

Primer
3

Pcr
primer design

The
pcr suit

  The Computational tools are mostly used for responsible
structural, characterization of genes, and it is also responsible physiochemical
properties of proteins, phylogenetic analyses, and performing simulation. It
also knows the work of biomolecule interact in a living cell. Even though these
tools cannot generate enough information as a reliable as experimentation,
which it is costly, time consuming ,however, the  analyses in silico can still facilitate that  reach an informed decision for showing a
experiment that is costly.

 A molecule that is druggable it must have
certain ADMET (absorption, distribution, metabolism, excretion, and toxicity)
properties that is pass through clinical trials. If a compound that does not
have required ADMETs, it is rejected. These failures are avoid to use different
bioinformatics tools that have been developed to predict ADMET properties. It allows
researchers to screen a large number of compounds that is to select most
druggables molecule before launching of clinical trials 5.

 We are know that biological activities are the
result of molecular interactions that is happen in a time-dependent manner. MDS
is a Molecular Dynamics simulation, it is a set of bioinformatics tools, time dependent
behaviour of a molecule could be studied it .The MDS techniques is provide
complete information on the fluctuations, dynamic processes like ion transport,
and small- and large-scale conformational changes of proteins, nucleic acids,
and that complexes that will be occurring in biological systems. It also
provide purpose of structures from experimental approaches like XRD and NMR
spectroscopy.  MDS tools also  used to gaining insights into situations
where the use of  experimental means is
not possible.

For example, we will determine
which serine residues is  take part in
phosphorylation of starch branching enzyme IIb (SBEIIb) most authors used MDS
combine with site-directed mutagenesis and mass spectroscopy. This study was able
us to control that phospho-Ser297 forms a constant salt bridge with Arg665, it
is part of a conserved Cys-covering domain in plant branching enzymes. These
study provides implications for explaining biological character of the enzyme
in starch biosynthesis in higher plants that is to yield-improvement perceptions
6

BLAST is
a basic local alignment search tools that is perform a correct method through
its use of heuristic, the current blast software speed is supported for very
suboptimal for very long queries or databases sequence. BLAST is a sequence
similarity search programs, it is used to search a sequence databases for
method to query sequences. It provides a expected value of statistical information
about the significance of each alignment 7. BLAST is one of the more popular
bioinformatics tools. Researchers used blast to search locally, custom
databases and performing searches in bulk. The BLAST application were available
to the public in late 1997. It is a pant of NCBI c toolkit and it is supported
a number of platform that includes LINUX, UNIX and Microsoft window 8.

UNIPRO UGENE is a multiplication open source
software its main goal is to assist molecular biology in bioinformatics to
manage analyse and it visualise their data. UGENE is reading and writing in
> 20 popular biological data formats.it is capable of working with local
files and assessing data from key biological data formats. it allows the
visualization of biological objects such as DNA and RNA and protein sequence
alignment, Phylogenatics trees and chromatograms.

 We will take the opportunity to develop
various tools of bioinformatics to a non-specialist reader to help useful
information regarding his/her project. WE have choose only those areas where
these tools could be mostly use to get useful information from biological data.
These areas most be included analyses of DNA/protein sequences, phylogenetic
studies, calculating 3D structures of protein molecules, it is used in molecular
interactions and simulations as well as drug designing.

 

Application of bioinformatics tools

 

Bioinformatics

Application of bioinformatics tools in
various areas of biological sciences

 

 

 

 

Conclusion and Future
Prospects

 IN the end I conclude that Bioinformatics is a
young discipline and it has progressed very fast in the last few years. It has
made it use to test our hypotheses virtually and it allows to take a good and
an informed decision before launching costly experimentations. Therefore, it
will be continue to the hunt for finding a better package for solving the given
problems. It is clear that the future research will be helped largely by the
availability of databases, which could be either generic or specific. The
bioinformatics tools and software packages will be able to give results that
are more accurate and thus more reliable interpretations. In the field of
bioinformatics development include its future contribution to functional
understanding of the human genome, it wil be leading to enhanced discovery of
drug targets and individualised therapy. So bioinformatics and other scientific
disciplines have play very important role in the welfare of mankind.

 

 

Reference

1. Mount DW (2004) Sequence and
genome analysis. New York: Cold Spring.

2. Hesper B, Hogeweg P (1970)
Bioinformatica:een werkconcept. Kameleon 1: 28-9.

3. Hogeweg P (2011) The roots of bioinformatics
in theoretical biology. PLoS Comput Biol7: e1002021.        

4. Peitsch MC (1996) ProMod and
Swiss-Model: Internet-based tools for automated comparative protein modelling.
Biochem Soc Trans 24: 274-279.

5. Dibyajyoti S, Bin ET, Swati P
(2013) Bioinformatics: The effects on the cost of drug discovery. Galle Med J
18: 44-50.

6.Makhmoudova A, Williams D, Brewer
D, Massey S, Patterson J, et al. (2014) Identification of multiple
phosphorylation sites on maize endosperm starch branching enzyme IIb, a key
enzyme in amylopectin biosynthesis. J Biol Chem 289: 9233-9246

7. Altschul, S.; Gish, W.; Miller,
W.; Myers, E.; Lipman, D. (1990). “Basic Local Alignment Search
Tool”.

8. www.NCBI
toolkit

9.
Konstantin Okonechnikov  Olga
Golosova  Mikhail Fursov  the UGENE team

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