8. David M.A. Martin, Michele Clamp, Geoffrey J. Barton;

8.      Chris Burge, Samuel Karlin; Prediction
of complete gene structures in human genomic DNA. Journal of Molecular Biology, Volume 268, Issue
1, 25 April 1997, Pages 78-94, https://doi.org/10.1006/jmbi.1997.0951.

7.      Duncan Hull, Katy Wolstencroft, Robert Stevens, Carole
Goble, Mathew R. Pocock, Peter Li, Tom Oinn; Taverna: a tool for building and
running workflows of services. Nucleic Acids Research, Volume 34,
Issue suppl_2, 1 July 2006, Pages W729–W732, https://doi.org/10.1093/nar/gkl320.

We Will Write a Custom Essay Specifically
For You For Only $13.90/page!


order now

6.      Robert C. Edgar; MUSCLE: multiple sequence alignment with
high accuracy and high throughput. 1792-1797 Nucleic Acids Research, 2004,
Vol.32, No.5 DOI: 10.1093/nar/gkh340.

5.      Andrew M. Waterhouse, James B. Procter, David M.A.
Martin, Michele Clamp, Geoffrey J. Barton; JALVIEW Version 2—a multiple
sequence alignment editor and analysis workbench. Bioinformatics,
Volume 25, Issue 9, 1 May 2009, Pages 1189–1191, https://doi.org/10.1093/bioinformatics/btp033.

4.      Timothy L. Bailey, Nadya Williams, Chris Misleh and
Wilfred W. Li; MEME: discovering and analyzing DNA and protein sequence motifs.
Nucleic Acids Research, 2006, Vol. 34, Web Server issue W369–W373
doi:10.1093/nar/gkl198.

3.      Sudhir Kumar, Glen Stecher, Daniel Peterson, Koichiro
Tamura; MEGA-CC: computing core of molecular evolutionary genetics analysis
program for automated and iterative data analysis, Bioinformatics,
Volume 28, Issue 20, 15 October 2012, Pages 2685–2686, https://doi.org/10.1093/bioinformatics/bts507.

2.      Sievers
F., Higgins D.G. (2014) Clustal Omega, Accurate Alignment of Very Large Numbers
of Sequences. In: Russell D. (eds) Multiple Sequence Alignment Methods. Methods
in Molecular Biology (Methods and Protocols), vol 1079. Humana Press, Totowa,
NJ.

1.      Mehmood MA, Sehar U, Ahmad N (2014) Use of Bioinformatics
Tools in Different Spheres of Life Sciences. J Data Mining Genomics Proteomics
5: 158. doi:10.4172/2153-0602.1000158.

References

 

Sr no.

Tool

Description

References

1.

CLUSTAL Omega

Multiple
sequence alignment of biological sequences using algorithms.

2

2.

MEGA

Reconstruct or
rebuild evolutionary relatedness among organisms.

3

3.

MEME

To find motifs
in biomolecules, domains in proteins and protein binding sites in DNA.

4

4.

JALVIEW

To edit,
analyze and visualize the multiple sequence alignment in biological
sequences, predict secondary structures in protein molecules.

5

5.

MUSCLE

Alignment of
protein sequences by multiple sequence alignment, phylogenetic analysis and
predict protein structures.

6

6.

Taverna

Comforts
bioinformaticians who are not skillful in web services and programming by
providing interface between different tools and databases.

7

7.

GENSCAN

Find whole
genome structures of human, predict exons, introns, transcriptional,
translational signals and intergenic regions, find gene or multiple genes in
DNA.

8

 

 

It is such a tool used to find and search whole structures
present in genomic DNA of humans. GENSCAN used to predict exons, introns,
transcriptional, translational signals and intergenic regions in the DNA. Gene
or multiple genes present in DNA can also be predicted by using this tool. This
tool proved to be accurate as it predicted 75 to 80 % exons precisely. (Chris Burge, Samuel Karlin, 1997) 8.

7.    
GENSCAN

Taverna has number of uses in constructing and performing
a sequence of activities that comforts bioinformaticians who are not skillful
in web services and programming languages. It provides interface between
bioinformaticians and web services that helps to communicate between different
tools and databases for sequence analyses. Taverna has many services and one of
them provided by INSDC (http://www.insdc.org/ ). (Duncan Hull et.al, 2006) 7.

6.    
Taverna

It is a protein sequence alignment tool used to build
alignments of protein sequences by multiple sequence alignment with great
accuracy. It is reported to be the fastest sequence alignment tool compared
with other alignment tools e.g., T-Coffee, CLUSTALW etc. It has wide range of
uses including phylogenetic analysis, to predict protein structure etc. The
most important thing of this tool is to show the evolution of sequences by
graphs. (Robert C. Edgar, 2004) 6.

5.    
MUSCLE

It a tool used to edit, analyze and visualize the
multiple sequence alignment of biological sequences and refine the sequences. It
is used to align the sequences and predict the secondary structures of the
protein molecules. It shows the alignment results by showing figures and
construct phylogenetic trees of sequences. JALVIEW 1.0 is not able to analyze
the huge and detailed tasks, so JALVIEW 2 is constructed by bioinformaticians
to perform greater tasks. (Andrew M.
Waterhouse et.al, 2009) 5.

4.    
JALVIEW

It is a bioinformatics tool used to find out motifs in
biological sequences of biomolecules e.g., proteins and DNA. It is also used to
discover domains in proteins and protein binding sites in DNA. It can also be
used to find out repeated sequences in proteins and DNA when query sequences
are submitted into it. (Timothy L.
Bailey et.al, 2006) 4.

3.    
MEME (Multiple EM For Motif Elicitation)

It
is a bioinformatics tool used to reconstruct or rebuild evolutionary
relatedness among the species or organisms. MEGA’s important feature is the use
of graphical user interface (GUI), that shows the graphical representation of
the given data, phylogenetic trees and results. (Sudhir Kumar et.al, 2012) 3.

2.    
MEGA
(Molecular Evolutionary Genetics Analysis)

CLUSTAL Omega is a latest version of the
CLUSTAL programs for multiple sequence alignment of biological sequences. It
uses algorithms for construction of guide trees. The software has proved to be
better than earlier CLUSTAL series and it has great precision. The larger alignments
can be done using this tool even on home computers. (Sievers
F., Higgins D.G., 2014) 2.

1.    
CLUSTAL
Omega

Bioinformatics tools for biological
sequence analyses

The
sequences are the information stored in DNA and proteins in the form of letters.
These letters are instructions and have specific arrangements given by the
nature to our DNA and from DNA to proteins. The nucleotides in DNA are
instructions that pass from generation to generation. The proteins are
macromolecules made of amino acid sequences and perform many functions of the
body. The sequences came into existence due to molecular attractions of
different molecules. Sequence analyses
is the comprehension of novel arrangement and characteristics of codes in a
biomolecule like nucleic acid and protein, that are responsible for their
operation and function. (Mehmood MA
et.al, 2014) 1. For carrying out sequence analyses, the sequences after retrieval from different
databases are refined and submitted to various tools that speculate their
features important for their function, structure and evolutionary history with
extreme precision. (Mehmood MA et.al,
2014) 1. The objective of this review is to encompass all the tools being
used for biological sequence analyses.

Introduction

x

Hi!
I'm Mack!

Would you like to get a custom essay? How about receiving a customized one?

Check it out